Skip to main content

Table 6 Transcriptome assemblies of kCombine based on Oases and Trinity in Cochliomyia macellaria with k=25 over different values of k-mer coverage cutoff c, with locus denoting the number of predicted locus, transcripts denoting the number of predicted transcripts, n50 denoting the N50 value of the length of predicted transcripts, blastx denoting the number of hits from translated BLAST search of predicted transcripts to different transcripts of the known Drosophila melanogaster transcriptome with e-value below 10−20, and memory denoting the physical memory requirement as a power of 2, with the value to the left of “+” indicating the memory requirement of the independent assembly of each individual library by Oases and Trinity, and the value to the right of “+” indicating the memory requirement of the merging step by kCombine

From: A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms

c Locus Transcripts n50 Blastx Memory
kCombine(Oases)      
10 60477 140681 2502 20385 256 GB + 4 GB
20 42334 101421 2349 20579 256 GB + 4 GB
50 30858 67217 1924 20101 256 GB + 4 GB
kCombine(Trinity)      
5 46342 153790 1961 22996 512 GB + 16 GB
10 34614 111379 1934 22874 512 GB + 16 GB
20 28756 85093 1567 22595 512 GB + 16 GB