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Table 1 Features supported by the tools

From: Benchmarking short sequence mapping tools

 

Bowtie

Bowtie2

BWA

SOAP2

MAQ

RMAP

GSNAP

FANGS

Novoalign

mrFAST

mrsFAST

Seed mm.

Up to 3

 

Any

Up to 2

Any

Any

     

Non-seed mm.

QS

AS

Count

Count

QS

Count

Count

Count

QS

Count

Count

Var. seed len.

> 5

 

Any

> 28

       

Mapping qual.

 

Yes

Yes

 

Yes

   

Yes

  

Gapped align.

 

Yes

Yes

PE

PE

 

Yes

Yes

Yes

Yes

 

Colorspace

Yes

 

Yes

 

Yes

   

Yes

  

Splicing

      

Yes

    

SNP tolerance

      

Yes

    

Bisulphite reads

     

Yes

Yes

 

Yes

Yes

 
  1. PE: paired-end only, mm.: mismatches, QS: base quality score, count: total count of mismatches in the read, AS: alignment score, and empty cells mean not supported.
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