GapFiller: a de novo assembly approach to fill the gap within paired reads

BMC Bioinformatics

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.

ISSN: 1471-2105