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.

Caboche et al.

Caboche et al. BMC Genomics 2014 15:264   doi:10.1186/1471-2164-15-264

Open Data