Table 4 Features supported by Bismark, BS-Seeker, BS-Seeker2, BSMAP, and VAliBS

O.S.

Linux,Mac

Linux,Mac

Linux, Unix, Mac

Linux, Unix, Mac

Linux

Seq.Plat.

I

I

I

I

I, 4

Input

FASTA/Q

FASTA/Q

FASTA/Q, qseq

FASTA/Q SAM/BAM

FASTA/Q

Output

SAM

SAM

SAM/BAM

SAM BAM Native

SAM

Min. RL

16

10

20

22

Max. RL

10 K

200

144

#Mis

Score

3

Score

15

Score

Indels

Score

0

Score

1

Score

Gaps

N

N

Y

N

Y

Align. Reported

U

U

B,U,S

B,R,U

A,B

Alignment

G, L

G

G, L

Parallel

SM

SM

SM

SM

SM

QA

Y

Y

N

N

Y

PE

Y

Y

Y

Y

Y

Vis

N

N

N

N

Y