Pollux: platform independent error correction of single and mixed genomes

BMC Bioinformatics

Table 2 Alignment comparison of corresponding uncorrected and corrected reads against the reference genome

	Corrected (Abundance (counts/kb))				Introduced (Abundance (counts/kb))
Platform (Run)	Total	Mismatches	Insertions	Deletions	Total	Mismatches	Insertions	Deletions
GS Junior (1)	81%	76% (0.33)	82% (2.28)	81% (0.81)	4%	11% (0.048)	2% (0.065)	6% (0.063)
GS Junior (2)	85%	79% (0.24)	86% (2.23)	83% (0.76)	4%	15% (0.044)	2% (0.059)	6% (0.050)
PGM (1)	88%	82% (1.68)	91% (7.67)	86% (7.10)	3%	2% (0.046)	2% (0.16)	5% (0.44)
PGM (2)	86%	80% (1.72)	90% (7.47)	84% (7.70)	4%	2% (0.052)	2% (0.16)	6% (0.52)
MiSeq	94%	95% (0.85)	10% (0.0015)	78% (0.007)	1%	1% (0.010)	4% (0.0007)	8% (0.0007)

All reads are sequenced from the same O104:H4 E. coli isolate. Corresponding uncorrected and corrected reads are aligned to the reference genome using SMALT. Incomparable alignments are removed. Corrected errors reflect alignment errors which are found in uncorrected reads but not in corrected reads. Similarly, introduced errors are a consequence of alignment errors found in corrected reads but not in uncorrected reads.

ISSN: 1471-2105