Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

BMC Genomics

Table 2 Description of mappers used in this study

Features of mappers used in this study
Name	Version	Algorithm	Mis.	Indels	Gaps	Report	Align.	Parallel	Qual.	Ref.
Bowtie2	2.0.4	BWT	Y	Y	Y	A	G,L	Y	Y	[16]
BWA	0.6.2	BWT	Y	Y	Y	A	G	Y	Y	[17]
BWASW	0.6.2	BWT	Y	Y	Y	AnyB	L	Y	Y	[18]
GSNAP	2012-12-20	HT	Y	Y	Y	A	G,L	Y	N	[19]
MOSAIK	2.1.73	HTR	Y	Y	Y	A	G	Y	Y	[20]
Novoalign	2.08.03	HT	Y	Y	Y	A	G	N	Y
PASS	2.02	HT	Y	Y	Y	A	G	Y	Y	[21]
segemehl	0.1.4-380	ESA	Y	Y	Y	A	G	Y	N	[22]
SHRiMP2	2.2.3	HT	Y	Y	N	A	G	Y	Y	[23]
SMALT	0.7.0.1	HT	Y	Y	N	A	L	Y	Y
SNAP	0.15	HT	Y	Y	Y	AnyB	G,L	Y	Y	[24]
SRmapper	0.1.1	HT	Y	N	N	AB	G	N	N	[25]
SSAHA2	2.5.5	HT	Y	Y	N	A	L	N	N	[26]
TMAP	3.2.2	BWT	Y	Y	Y	A	G,L	Y	Y	[27]

The column headed ‘version’ indicates the version of the mapper used in this study; the column headed ‘algorithm’ gives the algorithmic method used in the mapper. BWT, the reference genome was indexed with the Burrows–Wheeler transform; HT, the reference genome was indexed with Hash-Table; HTR, the reference genome and reads were indexed with Hash-Table; and ESA, the reference genome was indexed by enhanced suffix arrays. In the columns headed ‘mis.’ (mismatches), ‘indels’, and ‘gaps’, ‘Y’ indicates the algorithm allows mismatches, indels, and long insertions or deletions, and ‘N’ indicates otherwise. The column headed ‘report’ indicates the available report mode: ‘A’ for ‘all’; ‘AnyB’ for ‘any-best’; and ‘AB’ for ‘all-best’ mode. The column headed ‘align.’ ‘G’ (globally) indicates the reads were aligned end-to-end and ‘L’ locally indicates they were not. In the column headed ‘parallel’, ‘Y’ indicates the algorithm is multi-threaded, and ‘N’ indicates it is not. The column headed ‘qual.’ indicates if sequencing quality is taken into account by the mapper (‘Y’ for yes; ‘N’ for no). Bibliographical references are given in the last column.

ISSN: 1471-2164