 Research
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Improving the sensitivity of long read overlap detection using grouped short kmer matches
BMC Genomics volume 20, Article number: 190 (2019)
Abstract
Background
Singlemolecule, realtime sequencing (SMRT) developed by Pacific BioSciences produces longer reads than secondgeneration sequencing technologies such as Illumina. The increased read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and characterize the intraspecies variations. It also holds the promise to decipher the community structure in complex microbial communities because long reads help metagenomic assembly. One key step in genome assembly using long reads is to quickly identify reads forming overlaps. Because PacBio data has higher sequencing error rate and lower coverage than popular short read sequencing technologies (such as Illumina), efficient detection of true overlaps requires specially designed algorithms. In particular, there is still a need to improve the sensitivity of detecting small overlaps or overlaps with high error rates in both reads. Addressing this need will enable better assembly for metagenomic data produced by thirdgeneration sequencing technologies.
Results
In this work, we designed and implemented an overlap detection program named GroupK, for thirdgeneration sequencing reads based on grouped kmer hits. While using kmer hits for detecting reads’ overlaps has been adopted by several existing programs, our method uses a group of short kmer hits satisfying statistically derived distance constraints to increase the sensitivity of small overlap detection. Grouped kmer hit was originally designed for homology search. We are the first to apply group hit for long read overlap detection. The experimental results of applying our pipeline to both simulated and real thirdgeneration sequencing data showed that GroupK enables more sensitive overlap detection, especially for datasets of low sequencing coverage.
Conclusions
GroupK is best used for detecting small overlaps for thirdgeneration sequencing data. It provides a useful supplementary tool to existing ones for more sensitive and accurate overlap detection. The source code is freely available at https://github.com/Strideradu/GroupK.
Background
The increased read length enables thirdgeneration sequencing to close gaps in genome assembly [1, 2], reveal structural variations [3], and quantify gene isoforms with higher accuracy [4] in transcriptomic sequencing. In addition, using long reads holds promise in revealing the microbial community structure and deciphering intraspecies variation for microbial communities [5, 6].
Genome assembly using thirdgeneration sequencing data requires dedicated methods and tools. Existing genome assembly tools mainly utilize two types of graph models: overlap graph and de Bruijn graph. When the error rate is low, de Bruijn graph has the theoretical advantage that the graph size does not increase significantly with the sequencing coverage, which is usually high for Illumina datasets. For thirdgeneration sequencing data, the high error rate and low coverage make the overlap graph a sensible choice for genome assembly [7]. A key step in constructing the overlap graph is to identify read pairs that share overlaps, which indicates that these reads are sequenced from the same loci in the underlying genome. Although there are a number of sequence alignment programs available for conducting overlap alignment [8, 9], a majority of them rely on dynamic programming and are too computationally expensive for high throughput sequencing data. Due to high error rates, existing short read overlap detection software using BWT (BurrowsWheeler transform) or hash table [10, 11] cannot be directly applied to long reads.
Related work
Two strategies are currently being employed to detect overlaps for errorprone long reads. One strategy tries to correct sequencing errors in PacBio (Pacific Biosciences) and ONT (Oxford Nanopore) data before overlap detection. There exist a number of sequencing error correction tools [7, 12]. Some of them rely on hybrid sequencing, which requires preparation of at least two sequencing libraries and several types of sequencing runs and thus is not costeffective for many applications. Others conduct error correction using long reads only. One representative method is described in Chin et al.’s hierarchical genomeassembly process HGAP [12], whose performance improves with higher read coverage. It is worth noting that for alignmentbased error correction methods such as the one in HGAP, an important step is to identify reads that can be aligned quickly. Essentially, techniques used for overlap detection can be used for alignment detection as well.
The second category bypasses the difficulty of error correction and identifies overlaps using raw reads. Various approximate similarity search methods have been applied on PacBio and ONT data [13]. They generally follow seedchainalign procedure [14]. Seedbased filtration step plays an essential role in controlling the tradeoff between sensitivity and computational efficiency. Usually, these methods use short string matches as the filtration step. A short string or kmer match requires exact matches of k consecutive characters between two sequences. Intuitively, overlapping reads tend to share more common kmers than nonoverlapping reads. Strategies that can quickly find the number of shared kmers can thus be applied. In this section, we summarize the main strategies of several stateoftheart overlap detection tools. We highlight the differences between our method and the existing ones in the following section.
MHAP [15], Minimap [14, 16], and DALIGNER [17] all use kmer matches for identifying candidate overlapping pairs. Due to the high error rate, usually only short kmers will be applied in order to achieve high sensitivity. However, identifying short kmer matches between all pairs of reads is computationally expensive. Thus, the leading tools employed different data structures and algorithms for estimating kmerbased similarity. MHAP converts long reads into sets of kmers and sketches using minHash. Then the similarity between reads is estimated using the compact sketches. Minimap also uses a compact representation of the original reads by keeping minimizers rather than all possible kmers of a read. Then collinear kmers will be clustered and used for checking possible overlaps. DALIGNER directly sorts kmers based on their positions and then utilizes merge sort to identify the number of shared kmers. As the sorting is cache efficient, DALIGNER is practically very efficient.
BLASR [18] was initially designed for mapping PacBio reads to a reference genome. It is also widely used as an overlap detection tool for PacBio data. BLASR uses BWT and FM index to identify short kmer matches and then clusters kmer matches within a given distance range. The clustered kmers are ranked based on a function of the kmer frequency. Only highly ranked clusters will be kept for downstream analysis.
Being different from the above tools, GraphMap [19] uses spaced seeds that allow matches of nonconsecutive characters. Spaced seeds were initially used in homology search for improving the tradeoff between sensitivity and filtration efficiency [20–22]. In particular, spaced seeds containing the pattern “11*” have high sensitivity in capturing homologous proteincoding genes because of the codon structure. However, designing optimal spaced seeds (i.e., deciding the positions of the wildcard characters) is NPhard [23, 24]. GraphMap empirically chooses two spaced seeds. Ideally, different sets of seeds may be designed for input data of different error profiles.
Overview of our work
The high error rates and also the different error profiles of PacBio and ONT data motivate us to use a more flexible seeding strategy called group hit criteria [25], which define a group of possibly overlapping kmers satisfying statistically derived distance constrains. For brevity, we will call the kmers set satisfying the group hit criteria as a “group seed”. A group seed was initially proposed and used for homology search. Given the error profiles, such as the estimated indels and mismatch probabilities, thresholds for grouping short kmers can be computed using the waiting time distribution and the onedimensional random walk [25]. A group seed can effectively handle all types of errors and is ideal to detect small overlaps. With group seeds, we can achieve high sensitivity using short kmers (e.g., 9mer) while still maintaining a desirable specificity.
In this work, we employ group seeds for detecting overlapping long reads for genome assembly. Our implementation, named GroupK, provides a complementary tool to existing methods for detecting small overlaps or overlaps compounded by high error rates of both reads. This ability enables our tool a sensible choice for genome assembly in metagenomic data sequenced by thirdgeneration sequencing platforms. As these community samples usually contain microorganisms with heterogeneous coverage, being able to identify small overlaps will be very important for reconstructing genomes of rare species.
Methods
GroupK is designed for improving the sensitivity of detecting small overlaps or overlaps with low identity. Currently, thirdgeneration sequencing data still has high error rates. The overlapping regions formed by two errorprone long reads can have lower sequence identity than mapping a long read against a reference genome. Figure 1 presents the histogram of the overlap size and the corresponding ratio of overlap size to the read length between two adjacent reads. The reads are simulated using PBSIM [26] from E. coli with three different coverages. As we know the position of each simulated read in the genome, the overlap size can be easily decided. Note that a read can form overlaps with multiple reads sequenced from the same region. However, the two figures are generated using overlaps between two adjacent reads, which define an “irreducible” edge [27] in an overlap graph. Thus, these overlaps can decide the continuity of the final genome assembly. The figures show that there are still substantial regions with small overlaps. For example, there are 45.46%, 34.76%, and 31.19% of the overlaps shorter than the 50% of the read length for data with coverage of 8X, 15X, and 30X, respectively. It will be ideal to detect relatively small overlaps to fully take advantage of the long reads for generating more complete assemblies.
Pipeline
Identifying small overlaps is computationally difficult. Thus, we use a carefully designed hierarchical filtration strategy to distinguish true overlapping reads from nonoverlapping ones. The pipeline of GroupK consists of three key steps: filtration, group seed matching, and chaining (Fig. 2). Filtration is used to reduce the search space by quickly identifying read pairs sharing a minimum number of kmers. High insertion/deletion error rates tend to produce short kmer matches on different diagonals. Thus, we adopt group seed matching to identify a group of short kmer matches in close proximity. There are two types of distance constraints. 1) The distance (number of nucleotides) between the kmers on xaxis and yaxis must be smaller than a given threshold; 2) the diagonal distance, which is the difference of the diagonals of two kmer matches, must be within a given range. Chaining is used to estimate the final overlap region. Figure 3 shows that applying group seed can remove a large number of random kmer hits while keeping the kmer matches within the overlapping region. When k=15, there are only two hits, and it is difficult to determine whether there is an overlap. When k=9, there is clearly a chain formed by hits in the overlapping region. However, there are also a large number of random hits. With group seed matching criteria, most of the random 9mer hits are filtered out. So the downstream analysis becomes more straightforward.
Estimate the expected number of kmers for the filtration stage
In this section, we analyze the expected number of random kmer hits between two reads and also kmer hits in overlaps. The analysis will be used for determining the kmer size and also other parameters for the filtration stage. Given two reads (S_{1} and S_{2}) with length L and error rate ε, we want to determine how many kmer hits we expect to find between S_{1} and S_{2}.
We first consider the case that S_{1} and S_{2} are not related (no overlap). By assuming that the bases in S_{1} and S_{2} are randomly distributed, the expected number of random kmer matches E[X_{r}] is roughly:
Note that this equation is different from the expected number of shared kmers in MHAP [15] because we distinguish kmer hits based on their locations rather than the kmers themselves. Also, we assume that overlapping kmers are independent.
In the second case of S_{1} and S_{2} forming an overlap, we estimate the expected number of kmer matches in the overlap by first computing P_{o}, which is the probability of observing a kmer match within the overlap. In the case of no sequencing error (i.e. ε=0), the probability of observing a kmer match at an aligned position in an overlap is simply 1.0. But in the practical case of ε>0, we need to consider two scenarios in order to determine the probability of observing two identical characters at an aligned position in the overlap: 1) the characters from S_{1} and S_{2} are correct; 2) the two characters from S_{1} and S_{2} are errors and are randomly substituted by the same character. The two cases are visualized in Fig. 4. So the probability is given by [15]:
Considering both random kmer matches and kmer matches in an overlap, the expected number of shared kmers between two overlapping reads is estimated by:
M is the size of the overlap. Note that the above equation slightly overcounts the number of kmer hits in an overlap because the random kmer hits inside the overlap may be counted twice with probability \(P_{\mathrm {o}} \cdot \left (\frac {1}{\Sigma }\right)^{k}\). (Also, we assume that the probabilities of substitution and insertion/deletion are on the same order and thus do not distinguish them in the above equation.)
As we are mainly interested in finding small overlaps or overlaps with low sequence identity, we plot the expected number of kmer hits with the overlap size being 1/4 of the read size in Fig. 5. In order to plot the figure, we compute E[X_{o}] and E[X_{r}] using the read lengths from a 15X E. coli PacBio dataset (the data of our second experiment in Results). We only consider reads of length above 2,000. These figures allow us to choose the appropriate threshold for kmercounting based filtration. For example, Fig. 5 shows the expected number of 15mers between reads of different error rates. E[X_{r}] started as 4 when ε=0.15. And, for larger ε, E[X_{r}] is even smaller. Thus, our default filtration threshold is two 15mers in order to ensure high filtration sensitivity. The implementation details of the kmer counting stage can be found towards the end of the “Methods” section.
Group hit criteria
Sequencing errors tend to produce short kmer matches. In addition, the insertion/deletion errors lead to kmer matches on different diagonals. Thus, instead of using relatively long kmers (such as 15 or 16mers) as existing tools do, we use a group of short kmers (such as 9mer) to accommodate the high insertion or deletion error rates. A group seed is a set of possibly overlapping kmer hits with statistically calculated constraints. The region containing group seeds is more likely to be inside an overlap than a single kmer hit. Reference [25] first introduced the group hit criteria and also derived the method to calculate the criteria statistically. We apply their method for overlap detection.
Assume that we have two reads S_{1} and S_{2} of length m and n, respectively. The numbers of kmers at different positions in S_{1} and S_{2} are m−k+1 and n−k+1, respectively. A kmer hit at position (i,j) is defined by S_{1}[i…i+k−1]=S_{2}[j…j+k−1], where i≤m−k+1 and j≤n−k+1. For two kmer hits at (i_{1},j_{1}) and (i_{2},j_{2}), their interseed distance D((i_{1},j_{1}),(i_{2},j_{2})) is the maximum of i_{2}−i_{1} and j_{2}−j_{1}. The kmer diagonal of a kmer hit at (i,j), d(i,j), is defined as j−i.
With these notations, the goal is to solve the following inequalities given confidence level 1−α defined by significance level α:
ρ and δ are integers we need to define the group hit criteria. For example, when α=0.05, our goal is to derive ρ and δ so that with 95% chance the interseed distance and the diagonal shift between two kmers in overlapping reads are at most ρ and δ, respectively.
Constraint on kmer distance We followed the model described in the article [25]. Runs of head in nindependent Bernoulli trials are used to model kmer matches, with the probability p for a match and (1−p) for a mismatch. In this model, a kmer match can be treated as k consecutive match runs with probability of p^{k}. From the waiting time distribution [28, 29], the probabilities of the interseed distance x of two kmers in an overlap are:
With the confidence level 1−α, ρ can be solved using following equation:
In the actual implementation we use α=0.05. Thus, there is 95% chance that the interseed distance of the two seeds in an overlap is less than the ρ calculated using Eq. 7.
Constraint on kmer diagonal distance The diagonal shift between two kmers, d(i_{1},j_{1})−d(i_{2},j_{2}), in two overlapping reads is caused by insertions and deletions. Note that the insertions and deletions are defined by comparing two reads, not between a read to a reference genome. So the insertion rate and deletion rate are treated equally.
The diagonal shift between two kmer hits can be modeled by a discrete onedimensional random walk model [25, 30]. The diagonal shift starts from 0. Let the steps of the random walk be l. Assume that the insertion and deletion rate is q across the whole read. Thus, the probability of a diagonal change is q, and the probability of staying in place is 1−2q. Also, we assume that in l steps, there are n_{i} inserted nucleotides (increase shift), n_{d} deleted nucleotides (decrease shift), and n_{m} matched nucleotides (no impact on shift). If the final diagonal shift is i, we have the following equations:
Reference [25] calculated the probability of obtaining a diagonal shift i after l steps in the random walk. According to Eq. (8), we have n_{i}=i+n_{d} and n_{m}=l−(i+2n_{d}). For a specific n_{d}, the probability of a random walk producing diagonal shift i can be calculated as the number of the possible paths \( \binom {l}{i+2n_{d}} \cdot \binom {i+2n_{d}}{i+n_{d}} \), times the probability product of all insertions, deletions, and no shift change at each step \( q^{n_{d}}q^{n_{d}+i}(12q)^{l\left (i+2n_{d}\right)} \). To calculate the probability of generating a diagonal shift i given l, P[i,l], we need to consider all possible values of n_{d}, which is from 0 (no deletion) to (l−i)/2 (no match). So we have:
To calculate δ, we sum up the probabilities \(\mathcal {P}[i, l]\) for i=0,±1,±2,...,±l until we reach the level 1−α. We refer the reader to the original article [25] for a more detailed discussion of the model and a practical implementation using generating functions.
In our experiment, we set the sequencing accuracy p=0.85 and the indel rate q=0.06, as PacBio reads tend to have higher indel rates than substitution error rates. Users can adjust these parameters based on their data properties. The significance level α is 0.05 and k is 9. Using Eq. 6, we can obtain ρ=54. Using Eq. 9 and ρ as an estimation of l, we can obtain δ=5 given ρ=54. Thus, when k=9, seeds with interseed distance D((i_{1},j_{1}),(i_{2},j_{2}))≤54 and diagonal shift d(i_{1},j_{1})−d(i_{2},j_{2})≤5 are clustered in the same group. In addition, if kmers (i_{1},j_{1}) and (i_{2},j_{2}) are in the same group and kmers (i_{2},j_{2}) and (i_{3},j_{3}) are in the same group, we will cluster (i_{1},j_{1}) and (i_{3},j_{3}) as well.
Group chaining
With group hit criteria, GroupK can find short similar regions. To identify the overlapping region, we aim to find a chain of group seed matches that maximizes the number of matched bases. We used the modified sparse dynamic programming for chaining [31, 32].
After generating a chain of group seed matches, we need to determine whether this chaining defines an overlap. We develop two criteria for this purpose. First, we calculate the expected number of matched bases from the group hit criteria, assuming that the chain covers the possible overlapping region with length L_{O} (L_{O} can be estimated by the extension of both ends of the optimal chain). We used the following equation to calculate the expected number of the matched bases n_{e}:
Where c is a coefficient to control the criteria, k is the size of kmer, ρ is the group hit criteria for the interkmer distance. We only report the chaining result if the number of matched bases n≥n_{e}. Second, we require that both reads have similar sizes inside the overlapping region.
In our experiment, we found that sometimes using the optimal chain generated from sparse dynamic programming may overestimate the overlap region, as shown in Fig. 6. This overestimation can jeopardize the sensitivity of detecting small overlaps. We fix this problem by only keeping the collinear group seeds, which are used to estimate the overlap size.
Implementation details of the major components
Filtration by kmer counts In the first step of our pipeline, we use kmer countingbased filtration to remove large numbers of read pairs that are not likely sequenced from the same loci on the underlying genome. We implemented kmer counting using a generalized suffix array and the derived longest common prefix (LCP) array. The generalized suffix array SA is created from the concatenated reads (delimited by special characters such as $) using a linear algorithm [33]. Then, we create the LCP using both the suffix array SA and the reversed suffix array SA^{′} [34, 35]. Let the sequence of concatenated reads be T. Following the definition of the reversed suffix array, for a suffix starting at position SA[i], we have SA^{′}[SA[i]]=i. For each position i in the LCP, LCP[i] contains the size of the longest common prefix between SA[i] and SA[i−1]. The key observation [33] for efficient computation of LCP[i] is: for a position j in T, if LCP[SA^{′}[j−1]] is L, LCP[SA^{′}[j]]≥L−1. The whole LCP array construction takes linear time to the size of T [33].
In order to count the shared kmers between reads and also report read pairs passing the kmer counting threshold, we use both LCP and an auxiliary data structure recording the read IDs (denoted as array readID). For a suffix starting at position SA[i], its read ID is at readID[i]. The pseudocode of finding the number of shared kmers can be found in Algorithm 1. In practice, we also count kmers between a read and the other read’s reverse complement.
Group seed match and chaining Any pair of reads that pass the above filtration stage will be used as input for finding group seed matches. All other pairs will be discarded. Currently, we are using the codes of YASS [36, 37] for finding the group seed matches. The program uses hashing table to find short exact matches and creates the groups of matches on the fly. It is our future work to reimplement group seed matching using more efficient indexingbased methods. Implementation of chaining algorithm has been modified from the program of global chaining algorithm in SeqAn library [38].
Time complexity analysis If we have N reads with average read length L, our text size is NL. Therefore, we have NL elements in the suffix array and the corresponding LCP array. For each suffix in the suffix array, suppose on average, it can form LCPs with m other suffixes with size above k, which is the size of kmer used in the kmercount filtration steps. So the time complexity of finding all the shared kmers for all possible reading pairs is \( \mathcal {O}(mNL) \). If k is large enough (e.g., k=15 and 11 in our experiment), we have m≪NL, so the time complexity will be dominated by NL.
For N^{′} read pairs that pass the filtration stage, let the average number of kmer hits for each pair be q. Sorting the hits will need \( \mathcal {O}(q\log q) \) and iterating through all hits to find groups is linear to q. For all the read pairs, the time complexity is \( \mathcal {O}(N'q\log q) \).
Assuming finally we have r group seeds, the chaining procedure has complexity in \( \mathcal {O}(r\log r) \) for each read pairs. For all the read pairs, the time complexity is \(\mathcal {O}(N'r\log r) \). It is practically very fast because the number of group seed matches is very small compared to the original seed hits (indicated by Fig. 3).
Results
We focus on evaluating the sensitivity and precision of overlap detection. We applied GroupK to three PacBio datasets and one ONT dataset: a simulated PacBio RSII E. coli sequencing dataset, a real PacBio RSII E. coli sequencing dataset, a PacBio RSII human foot metagenomic sequencing dataset, and an ONT E. coli (SQKMAP006) dataset. For simulated E. coli dataset, we have the true sampling position for each read as our ground truth. For the real E. coli dataset and human foot dataset, we determine the ground truth via BLASR’s [18] alignments against the reference genome.
We benchmarked GroupK’s performance with Minimap [16], Minimap2 [14], DALIGNER [17], MHAP [15], and GraphMap [19]. Those tools and methods are representative overlap detection tools for long erroneous reads from PacBio or ONT [13]. All the detailed parameters can be found at the website listed in “Availability of data and materials”. Our main metrics include: (1) sensitivity, which measures the ratio of the true overlaps identified by each program to the whole set of overlapping pairs; (2) precision, which quantifies the ratio of true overlap detected by each program to the total reported overlapping pairs; and (3) F1 score, which is the harmonic mean of sensitivity and precision. A reported overlapping pair is regarded as correct if it is also present in our ground truth. The detailed overlap region and overlap length were not considered in the current evaluation because these read pairs can go through a more accurate alignment program for generating the final overlap alignment. As we discussed in Background, our goal is to identify overlapping reads without using error correction. All tested tools will thus be applied to their raw data set.
Simulated E. coli dataset
We first evaluated the performance of our method on a simulated E. coli dataset. The dataset was generated using PBSIM [26] with E. coli K12 MG1655 as the reference genome [39]. The length distribution and the quality profile were derived from real PacBio P6C4 E. coli dataset [40]. The simulated dataset has 5620 reads, with average length of 8,344.78 bps and 14.5% average error rate (8.6% insertions, 4.4% deletions, and 1.4% substitutions).
From the report by PBSIM, we can obtain the exact locations where the simulated reads are sampled in the genome. This information provides us with the ground truth for reads’ overlaps so that we can calculate the sensitivity and precision.
Following the pipeline we discussed in Methods, we first used kmercounting as the filtration stage. According to Eq. 1, Eq. 3, and Fig. 5, we discarded all read pairs with less than two 15mer matches. The sensitivity of the filtration is 0.979 and only about 6% of read pairs are kept for downstream analysis.
We evaluated the performance of our tool by adjusting the group seed match criteria coefficient c, which is introduced in Methods. With the increase of c, sensitivity will become higher, and the precision will become lower. As shown in Fig. 7, GroupK can achieve 5 to 6% improvement on the sensitivity with similar precision to other overlap detection tools.
Running time and memory usage
We evaluated the running time and the peak memory usage of the tested tools in this experiment. We run all overlap detection tools with a single core of 2.4Ghz 14core Intel Xeon E52680v4 CPU and 32 GB memory requested from the HighPerformance Computing Center at Michigan State University. The performance is measured with the best F1 score. The results are reported in Table 1. For the memory usage, Minimap2 is the most efficient one but all others are comparable. GroupK is slower than other tools, partially because we use small kmers. We found that the bottleneck of our program is the group matching stage, which accounts for about 1200 of 1871 s. By implementing a more efficient indexingbased method, we expect to reduce the running time of this stage. For example, we can speed up kmer counting by adopting the method used in KMC [41].
Real PacBio E. coli dataset
After using the simulated dataset to evaluate our method’s performance, we applied GroupK to a real PacBio RS II (P6C4) E. coli dataset [40]. The coverage of the whole dataset is 150X. To test the performance of low coverage data, we sampled a 15X coverage dataset based on the read length distribution of the whole dataset. The dataset has 14,262 reads, with the average length of 4,882.09 bps and average error rate of 14.14% (error rate is estimated using quality score).
We applied BLASR to map the reads to the reference genome to estimate the ground truth (BLASR was run with parameters: minReadLength, 2000; maxScore, 1000; maxLCPLength, 16; minMatch, 12; m 4 and nCandidates/bestn set to 10 × sequencing coverage). The mapping result from BLASR may contain short alignments due to the repeat in the genomes. So when we determine the ground truth, we only consider the alignments that cover at least 80% of the read. By removing short noisy alignments, we can make sure the BLASR alignments are close to the underlying ground truth.
We used the same filtration setup adopted in the simulated E. coli experiment. Among all overlap detection tools we tested, GroupK still achieved the highest sensitivity with comparable precision (Table 2). With slightly higher precision, our sensitivity is 4% better than the next best tool, Minimap. Compared to the previous experiment, the difference in sensitivity is smaller. One reason lies in the construction of the ground truth dataset. In the simulated dataset, we used the sample positions of all reads to determine whether two reads form an overlap. Thus, that dataset can include reads with small overlaps or reads with higher error rates. In this dataset, our method discarded BLASR alignments with high error rates and the remaining alignments have higher similarities with the reference genome and thus produce fewer “hard cases”. As Minimap is the second best tool for this dataset, we further analyzed the performance of GroupK and Minimap on read pairs of different overlap size in the next section.
Performance with different overlap size We divide all overlapping pairs into bins of width 500 based on the overlap size. For example, the first bin has the read pairs with overlap sizes from 0 to 499, and the second bin has read pairs with overlap sizes from 500 to 999, and so on. For each bin, we compared the sensitivity of GroupK and Minimap using parameters yielding the similar precision in Fig. 8. For Minimap, we showed the result with the highest F1 score. For GroupK, we selected a parameter so that it achieves similar precision to Minimap (F1 score: 0.9241, sensitivity: 0.9344, precision: 0.9140). According to Fig. 8, GroupK has much better sensitivity when the overlap size is less than 2000. As we showed in Fig. 1, there are a significant number of overlaps with overlap size smaller than 2000 even for 30X coverage. Being able to identify small overlaps allows us to generate more complete assemblies using long reads. This is particularly useful for low coverage data, such as what we usually have in metagenomic datasets.
Human foot metagenomic dataset
One of the major utilities of our tool is to identify overlaps between reads in metagenomic data that are sequenced using the PacBio platform. For complicated microbial communities, metagenomic data containing only short reads poses serious computational challenges for assembly and the downstream composition/functional analysis. Long reads hold the promise to produce more complete and accurate microbial genome assemblies for the metagenomic dataset. In this experiment, we evaluated the performance of overlap detection for a mock metagenomic dataset constructed from a real human foot dataset [5]. A particular challenge for this experiment is the low coverage of the component species in the metagenomic dataset, which could be caused by sequencing throughput and complexity of the sample.
The human foot sample was sequenced by linear PacBio RSII TdT (terminal deoxynucleotidyl transferase). Sequences that can be mapped to the human genome were removed as hostderived DNA. According to the Supplementary Materials of [5], there are about 1,000 bacteria and viruses in this metagenomic dataset. However, we cannot evaluate the performance of overlap detection on all the reads from the 1000 microbes because the coverages of many species are too low to yield meaningful overlaps. In order to construct the ground truth, we need to align the reads against species with known reference genomes and reasonable coverage. Thus, we only choose reads satisfying the following criteria: 1) the reads are sequenced from a species with known reference genome; and 2) the coverage of the species cannot be too small (e.g., >3X coverage). Based on these criteria, we keep the reads sequenced from three bacteria: Corynebacterium aurimucosum (6.3X Coverage), Corynebacterium tuberculostearicum (8.5X Coverage), and Staphylococcus hominis (3.2X Coverage). The reads are recruited via BLASR. The alignment positions are used to determine which reads form an overlap. Note that Corynebacterium aurimucosum and Corynebacterium tuberculostearicum belong to the same genus and may contribute to the false positive overlap detection due to their shared regions. The average length of the reads is 1696.25 bps, which is much shorter than the reads in the previous experiments.
As this dataset contains much shorter reads, the expected number of kmer hits will change. Intuitively we need to use shorter kmers to ensure high filtration sensitivity. Using the read length distribution, we calculated E[X_{r}] (Eq. 1) and E[X_{o}] (Eq. 3) and determined the kmer countingbased filtration criteria. In this experiment, we only kept read pairs that share at least three 11mers.
For this mock metagenomic dataset, GroupK yielded significantly better performance than other tools on metrics including F1 score, sensitivity, and precision (Table 3). Compared to other tools, GroupK can produce much higher sensitivity without sacrificing precision, leading to the higher F1 score. Besides evaluating the performance of various tools on all the reads from the three species, we also reported the performance of different overlap detection tools on each single bacteria dataset without mixing with other species (Table 3). In these tools, GraphMap has high specificity for all three with sacrifice of sensitivity. However, GroupK still achieves the best performance overall. The comparisons suggest that our method has great potential to detect overlaps for data with very low coverage (around 5X). This will enable better assembly for PacBio sequenced metagenomic data, which will become more available with the advances of long read sequencing technologies.
Real ONT E. coli dataset
We also tested our method on one ONT dataset. We used downsampled 15X coverage 2D reads from the SQKMAP006 dataset as 2D reads provide higher quality than 1D reads. We followed the same pipelines we used for the real E. coli PacBio dataset. As 2D ONT reads have similar error rates to the PacBio reads, we expect that our tool can still achieve reasonable performance given the same setup for the PacBio dataset. Therefore, we used the same parameters as the ones we used for the PacBio E. coli dataset.
Among these tools, GraphMap was designed for ONT data, Minimap2 provides a specific setup for finding the overlap on ONT dataset. All other tools are not specifically designed for ONT datasets. GroupK achieves the best F1 score compared to other tools’ default setup while keeping the highest sensitivity (Table 4). This result suggests that our strategy is robust with different types of long reads.
Discussion
Seeding is a key step for overlap detection because of the high error rate of long reads. Successful seeding strategies should balance the sensitivity and the specificity to achieve the optimal performance. Popular seeding methods include maximal exact matches, spaced seeds, and gapped spaced seeds. However, to successfully find a hit between two reads, these methods still need either to find relatively long continuous exact matches (large kmer) or to find inexact matches following certain error patterns (spaced seed). Compared to these methods, group seed matching is more flexible as it requires multiple short exact matches without specifying the error patterns. This flexibility leads to high sensitivity, and meanwhile the specificity is still guaranteed with the group seed match criteria.
Currently the group seed matching step based on hash table is the bottleneck of our overlap detection pipeline. A new method that can improve the running time efficiency of this step is needed to make the algorithm achieve the same speed as other faster overlap detection tools.
Conclusions
In this work, we developed an overlap detection tool for thirdgeneration sequencing data. By adopting the group hit criteria to cluster a group of short kmer hits that satisfy statistically derived distance constrains, our method can improve the sensitivity of overlap detection without sacrificing precision. Our experimental results have shown that for datasets with low sequencing coverage, our program can detect significantly more overlapping pairs while keeping high precision. One utility of our approach is to detect small overlaps between long reads of rare species in a microbial community.
Abbreviations
 BWT:

Burrows–wheeler transform
 LCP:

Longest common prefix
 ONT:

Oxford Nanopore
 PacBio:

Pacific biosciences
 SMRT:

Single molecule real time sequencing
 TdT:

Terminal deoxynucleotidyl transferase
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Funding
Publication of this article was sponsored by NSF Grant IOS1740874 and City University of Hong Kong.
Availability of data and materials
The source code of GroupK is available at https://github.com/Strideradu/GroupK.
The experiment details are at https://github.com/Strideradu/GroupK/tree/master/experiment.
About this supplement
This article has been published as part of BMC Genomics Volume 20 Supplement 2, 2019: Selected articles from the 17th Asia Pacific Bioinformatics Conference (APBC 2019): genomics. The full contents of the supplement are available online at https://bmcgenomics.biomedcentral.com/articles/supplements/volume20supplement2.
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YS proposed the original idea. YS and ND both designed the algorithm and the experiments. ND implemented the main algorithms, conducted the experiments, and analyzed the data. JC implemented the LCP array algorithm. All Authors wrote, read and approved the manuscript.
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Du, N., Chen, J. & Sun, Y. Improving the sensitivity of long read overlap detection using grouped short kmer matches. BMC Genomics 20 (Suppl 2), 190 (2019). https://doi.org/10.1186/s128640195475x
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DOI: https://doi.org/10.1186/s128640195475x