Last year I wrote a blog post "BLAST XML output needs more love from NCBI", and in the numerous updates to this, tracked the NCBI outreach and then release of BLAST XML 2.
The new output format was included in BLAST+ 2.2.31 as output format 15, without any kind of beta release for user feedback. Later than planned, I was able to give this a try during the Galaxy Community Conference 2015 Hackathon. Sadly the worries voiced on the OBF Bio* mailing lists were well founded.
In part because XML is so verbose, it is nice to be able to parse it as a stream - meaning capturing the output via stdout and Unix pipes. That appears to be "broken". In fact, producing a bundle of XML files using XInclude seems a recipe for trouble.
2015-07-04
NCBI working on SAM output from BLAST+
Recently NCBI BLAST+ 2.2.31 was released, and it contains an undocumented "Easter Egg" - this is still very rough around the edges but they're working on SAM format output!
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