Quality scores

[matsen]

Can we incorporate quality scores into partis? What sorts of scores can we expect to get from Adaptive? Stay tuned..

[krdav]

I am just leaving a comment on that:
It would be awesome to incorporate quality scores into an already great software. The competitor (SODA2) seems to do this already:
http://bioinformatics.oxfordjournals.org/content/26/7/867.full

However, how they use it is not very clearly stated and since SODA2 looks to be unsupported and no source code is provided it is hard to tell what they did. It seems like SODA2 has been succeeded by Cloanalyst:
http://www.bu.edu/computationalimmunology/research/software/
And they provide a Windows installer, but how are using Windows OS to do bioinformatics? I need to run things on millions of sequences and that requires a Linux cluster.

/Kristian