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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
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