Eric Boyden

I was looking for a java-based alternative to either cutadapt or ngmerge, and bbmerge seems to be able to do much of what both other tools can do (primarily I was looking for fixed read trimming, quality trimming, and paired read dovetail trimming). A few suggested improvements: * Allow simultaneous fixed trimming and q-trimming. Right now it seems like q-trimming supercedes fixed trimming if both are specified, regardless of which end you want to trim in each case; but there are situations where...

I was looking for a java-based global short-read aligner and this software performs excellently, with lots of neat features that many other aligners lack. In descending order of priority, here are some ideas for improvement: * Update SAM spec to v1.6 (currently 1.3/1.4), primarily to produce an updated @HD line to indicate query grouped output (GO:query). Many downstream tools (e.g. some fgbio tools) rely on this and won't work unless this is explicitly specified, and resorting just to add this annotation...