No More Maq?

Another grad student at the GSC forwarded an email to our mailing list the other day, which was in turn from the maq-help mailing list. Unfortunately, the link on the maq-help mailing list takes you to another page, which incidentally (and erroneously) complains that FindPeaks doesn't work with Maq .map files - which it does. Instead, I suggest checking out this post on SeqAnswers from Li Heng, the creator of Maq, which has a very similar message.

The main gist of it is that the .map file format will be deprecated, and there will be no new versions of the Maq software package in the future. Instead, they will be working on two other projects (from the forwarded email):

1. Samtools: replaces maq's (reference-based) "assembly"
2. bwa: replaces maq's "mapping" for whole human genome alignment.

I suppose it means that eventually FindPeaks should support the Samtools formats, which I'll have to look into at some point. For those of you who are still using Maq, you may need to start following those projects as well, simply because it raises the question of long-term Maq support. As with many early generation Bioinformatics tools, we'll just have to be patient and watch how the software landscape evolves.

It probably also means that I'll have to start watching the Samtools development more carefully for use with my thesis project - many of the tools they are planning seem to replace the ones I've already developed in the Vancouver Short Read Alignment Package. Eventually, I'll have to evaluate both sets against each other. (That could also be an interesting project.)

While this was news to me, it's probably no more than the expected churn of a young technology field. I'm sure it's not going to be long until even the 2nd generation sequencing machines themselves evolve into something else.