Table 4

Validation of GapFiller's output on GAGE datasets

Organism

Library

Avg contig length (bp)

Aligned contigs

Aligned length

Genome cov


S. aureus

Fragment

S.j. + fragment

182

3648

99.48%

98.74%

99.47%

98.76%

98.12%

95.00%


R. sphaeroides

Fragment

S.j. + fragment

188

3736

99.91%

98.20%

99.92%

98.22%

98.65%

74.12%


The experiments performed with both short jump (s.j.) and fragment libraries are done by picking the seeds from the short jump library only. We state that a contig is aligned against the reference if the alignment is a single hit covering 100% of contig's length and the percentage of identity is at least 95%. The statistics are computed on trusted contigs.

Nadalin et al. BMC Bioinformatics 2012 13(Suppl 14):S8   doi:10.1186/1471-2105-13-S14-S8

Open Data