Pollux: platform independent error correction of single and mixed genomes

BMC Bioinformatics

Table 1 The number of corrections reported and low-information reads removed by Pollux

	Number	Total number	Corrections				Reads
Platform (Run)	of reads	of bases	Mismatches	Insertions	Deletions	Homopolymers	removed
454 GS Junior (1)	135,992	70,999,968	24,100	164,198	56,144	17,221	1%
454 GS Junior (2)	137,528	71,710,564	21,004	167,999	53,947	13,535	1%
Ion Torrent PGM (1)	2,483,868	303,579,279	610,872	2,609,205	1,863,522	1,106,908	11%
Ion Torrent PGM (2)	2,154,577	260,017,346	561,024	2,215,086	1,765,495	968,961	13%
MiSeq	1,766,516	250,356,566	250,896	1,893	3,349	0	1%

All reads are sequenced from the same O104:H4 E. coli isolate. Substitution, insertion, deletion, and homopolymer corrections are performed on all data sets except for MiSeq, for which we do not perform homopolymer corrections. The percentage of reads which were removed as a consequence of more than 50% unique k-mers is provided under Reads Removed.

ISSN: 1471-2105