Sunday, 20 November 2011

[Bio-bwa-help] color-space support may be dropped in version 0.6

I think that bwa being able to support color space is a boon for analyzing solid data on ram limited machines.

Or on galaxy, which has only color space support on their test server ...

If bwa drops solid support then the remaining opensource options off the top of my head are bfast and bowtie.

There's also novoalign and bioscope (non open source )

But the drop for might also reflect a decrease in solid data in the wild ...

Possibly due to Life Tech push for Ion Torrent ...

What are your views?

On 20 Nov 2011 03:29, "Heng Li" wrote:
> The color-space alignment is not working in 0.6.0. Perhaps it is not so hard to make it work again, but bwa may not work well with solid reads all the time. Actually I have never evaluated this myself. 0.5.10 should work solid data.
> Any objections? Do you think it is worth keeping the color-space support in bwa?
> Thanks,
> Heng
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  1. Dear Heng,

    We would really appreciate if this option is supported in the future. We are using BWA for solid data in three locations running 7 solids at the moment and we are not very keen to switch to Lifescope of bfast since we developed automated and integrated pipelines.

    Ies Nijman
    Utrecht, Utrecht medical center, Wilh. Childrens hospital & hubrecht institute

    1. Hi Ies

      I am sorry to inform u
      From: "Heng Li"
      Date: 24 Nov 2011 11:38

      Thanks for all the replies. I will disable the color-space support in the 0.6.x branch, but leave non-functional source code in the files (though this is not my style). In future, I may re-evaluate the necessity of supporting color-space alignment in the 0.6.x branch. People who use bwa for color-space alignment may continue to use 0.5.10. 0.5.10 is as accurate as 0.6.x. It may be slower but just a little bit.

      Thank you all,



Datanami, Woe be me