Langmead at 15:38, 16 February 2009

2009-02-16T15:38:32Z

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'''Recent work.'''

Snapshot:

I'm working hard on getting paired-end support into Bowtie. I've settled on the best technique for doing this and I've implemented it in the -v 0 and -v 1 (no mismatches, one-mismatch resp.) alignment modes. I am now testing it, hoping to release a new version of Bowtie in the next couple days.

Outline of future work:

* Bowtie
** Paired-end support
*** Settled on a "mixed-mode" paradigm: find anchor mates in BW space, find opposite mates in reference space
**** Index becomes larger to accommodate the reference text (2.2 GB -> 2.9 GB for human)
**** Speed is about 2x slower than if all the mates were aligned in single-end mode
**** Default mode is "best-effort" - if you want Bowtie to bend over backwards to report all non-concordant pairs, that will be much slower but it can be activated from the command line
** Gapped alignment
** Mapping qualities
*** A la Maq
** Color space
* Crossbow
** Already have some results using some 1000-Genomes data: about 1 hr to align about 14.5x coverage for human
** Would like to do another run that includes paired-end reads and for which there is a trusted set of called SNPs

Cbcb:Pop-Lab:Ben-Report - Revision history

Langmead at 15:38, 16 February 2009