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Table 5 Comparison of the assemblies obtained for E. coli and S. cerevisiae from either uncorrected or corrected PacBio reads

From: Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

  E. coli (k=64) S. cerevisiae (k=51)
Statistical metrics Corrected Uncorrected Corrected Uncorrected
Number of contigs 2349 1721 61496 39127
Number of contigs ≥ 1 kbp 321 0 1657 0
Genome coverage (%) 98 0 91 0
Total length (Mbp) 4.71 0.12 15.00 2.39
Largest contig (bp) 93000 127 52444 378
GC (%) 50.19 3.77 38.75 40.00
N50 23473 69 6943 57
  1. The genome coverage accounts only for contigs longer than 1kbp. With uncorrected reads, the N50 remains close to the k-mer length (whatever the value of k); this strongly suggests that ABySS fails to assemble uncorrected reads. On the contrary, the metrics with corrected PacBio reads indicate that it yields satisfactory assemblies for both genomes