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Table 2 Comparisons of transcriptome assemblies of SOAPdenovo-Trans, Trans-ABySS and ASplice in model organisms over different values of k and k-mer coverage cutoff c

From: A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

S. pom SOAPdenovo-Trans Trans-ABySS ASplice
    total unique mem    total unique mem splicing   total unique mem
k_c locus N50 hits hits (GB) trans N50 hits hits (GB) graphs N50 hits hits (GB)
25_10 3267 4455 7343 4230 10 21215 2854 28376 4400 3 5859 3032 5271 4650 9
25_20 3393 3795 7153 4341 10 14193 2880 19541 4284 3 5231 2723 4941 4579 9
25_50 3747 3025 8174 4513 10 8748 2317 10686 4370 3 5163 2210 5002 4580 9
31_10 3366 4164 8481 4342 10 20569 2977 33192 4323 4 5580 3005 5148 4611 9
31_20 3470 3590 7864 4418 10 13701 3045 22303 4158 4 5076 2625 4956 4565 9
31_50 3891 2788 8783 4576 10 7972 2421 10259 4284 4 5103 2088 5080 4620 9
A. tha SOAPdenovo-Trans Trans-ABySS ASplice
    total unique mem    total unique mem splicing   total unique mem
k_c locus N50 hits hits (GB) trans N50 hits hits (GB) graphs N50 hits hits (GB)
25_10 18980 1705 80644 21614 17 348069 460 383663 21715 7 103450 344 92605 21487 10
25_20 16327 1622 71684 20239 17 159952 772 139875 20213 7 71419 561 66645 20033 9
25_50 13384 1472 53209 17788 17 66058 948 70136 17544 7 43407 778 42396 17535 9
31_10 19604 1700 74854 20952 17 350165 578 525359 21422 7 92665 444 88408 21288 10
31_20 16882 1605 62748 19516 17 141642 948 181322 19838 7 58877 760 56869 19691 9
31_50 13660 1438 42763 16990 17 54189 1083 75863 17050 7 35448 973 34906 17030 9
D. mel Trans-ABySS   ASplice
    total unique mem splicing total unique mem
k_c trans N50 hits hits (GB) graphs N50 hits hits (GB)
25_10 135048 1192 179499 12989 27 99930 728 51854 12322 11
25_20 83303 1693 102591 12848 27 60662 1328 35402 12245 10
25_50 47341 2082 58523 12453 27 36093 1874 26130 11921 9
31_10 113805 1547 225887 13025 30 77439 1203 45278 12453 11
31_20 70061 2029 124050 12787 30 45645 1952 28616 12259 10
31_50 41210 2296 64736 12337 30 32593 2085 24093 11861 9
  1. The predicted units are locus for SOAPdenovo-Trans that is represented as a splicing graph containing nodes and edges, transcript (trans) for Trans-ABySS that is a linear concatenation of constituent nodes, and splicing graph for ASplice. For SOAPdenovo-Trans and ASplice, N50 denotes the N50 value of the length (in nucleotides) of the longest path in each splicing graph. For Trans-ABySS, N50 denotes the N50 value of the length of a predicted transcript, and only predicted transcripts of length at least 100 are retained. Total hits denotes the total number of hits from nucleotide BLAST search of nodes to the transcriptome of the same organism. Isoforms are considered to be the same gene. Only the top hit with E-value below 10−7 is considered. Hits from nodes within the same predicted unit to the same gene are counted only once. Unique hits denotes the number of unique hits to different genes. Mem (GB) denotes the physical memory requirement in gigabytes over all stages of each algorithm
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