Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data

BMC Bioinformatics

Table 3 Human bisulfite read experiment

Evaluation metric	GNUMAP-bs	Novoalign	BSMAP	Bismark	Bismark-bt2	LAST	BRAT-BW
All chr22:
Reads Aligned	1.57M	1.65M	1.34M	1.31M	1.21M	3.02M	0.98M
CGs Covered	330K	336K	330K	310K	299K	373K	275K
CG read coverage	6.3	6.1	5.8	5.8	5.7	7.6	5.0
HEP overlap:
CGs Covered	7,902	7,802	7,747	7,561	7,331	8,606	6,690
Correlation	0.887	0.889	0.887	0.888	0.895	0.882	0.894
Concordance	0.869	0.867	0.865	0.867	0.872	0.858	0.872
CG Read coverage	4.6	4.5	4.4	4.3	4.3	4.9	3.7

Study of 162.3 M Illumina BSRs on human chromosome 22 (chr22) from a human donor sample. The top rows show the overall mapping efficiency, including covered CGs sites and read coverage aligned to chr22. The bottom rows show the consistency of each mapping result with known methylation levels at 13,563 CGs sites on chr22 available from the HEP database. The concordance statistic is defined as the fraction of overlapped CGs covered by the aligner with HEP CGs for which the methylation prediction error was smaller than 0.25.

ISSN: 1471-2105