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!

2015-06-01

PrePrint: SAM/BAM format v1.5 extensions for de novo assemblies

Here's a little back-story on my latest preprint (based on my email to samtools-devel), which went live on the biology preprint server bioRvix at the end of last week:
SAM/BAM format v1.5 extensions for de novo assemblies.
Peter J. A. Cock, James K. Bonfield, Bastien Chevreux, Heng Li.
bioRxiv DOI: 10.1101/020024
The current version is a terse three pages (trying to meet an "application note" page limit), but nevertheless should clarify the intended usage of these parts of the SAM/BAM specification.

2015-02-02

BLAST+ rejecting query files with zero sequences

This is another brief NCBI BLAST+ bug report blog post, about a regression in BLAST+ 2.2.29 which will be breaking existing pipelines around the world. The problem is a new "feature" which treats an empty query file as an error.

2014-12-23

BLAST+ Christmas Wish List

Dear Santa,

Please could you ask the Elves at the NCBI to deliver the following BLAST+ feature requests for Christmas 2014?

Thank you,

Peter

P.S. Do they think I have been naughty or nice with my BLAST blog posts?

2014-11-26

Column headers in BLAST+ tabular and CSV output

In the last couple of years, my preferred BLAST output format has switched from BLAST XML to plain tabular output. The main reason for this it is easier to parse, and now gives easy access to more fields - BLAST+ 2.2.28 added descriptions and taxonomy output to the tabular and CSV output, but the cumulative effect is BLAST XML has been lagging behind.

However, there is a simple change the NCBI could make to greatly improve the usability of the tabular or CSV output - label the columns with a header line! This is vital meta-data: No-one should be forced to guess-the-columns when presented with a data file.