flexible aligners

[bogdan]

Dear all,

please could you let me know the NG-seq aligner that is both fast and very flexible in terms of the insertions/deletions/mismatches ? thanks,

Bogdan

[volks]

if you are talking about small indels my choice would be BWA.

[zee]

Novoalign (www.novocraft.com) is also worth looking at. It offers a few more user-friendly options and alignment features than BWA.

There is also BFAST, and stampy.

if you are talking about small indels my choice would be BWA.

[nilshomer]

SHRIMP2 too.

[gaffa]

Stampy is good for aligning divergent reads with indels - it is not fast however, but it can be run in hybrid-mode with BWA to speed things up.

[dreesbl]

@bogdan

If you're interested, Spiral Genetics is launching a remote NGS analysis software pipeline that includes a fast-running gapped aligner that is a distributed adaptation of BWA's functionality. We're looking for researchers to test its performance with their data. You could run your reads single and run them double to see the effects on your downstream results. You can contact me via email or with a direct message through the forum if you're interested.

[email protected]

https://www.spiralgenetics.com