[Samtools-devel] SAM/BAM format v1.5 extensions for de novo assemblies

[Peter C. <p.j...@go...>]

Hello all,

Some of you spotted this preprint going up on bioRvix on Friday:

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

http://dx.doi.org/10.1101/020024
http://biorxiv.org/content/early/2015/05/29/020024

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.

This manuscript has been in progress since 2012, in parallel with
the associated file format change discussions all held openly
here on the samtools-devel mailing list, and "samtools depad"
work on GitHub.

My apologies to my co-authors, the long delays are my fault.
After getting useful comments from an internal pre-submission
review (thank you to colleagues at the James Hutton Institute),
I should have posted the current preprint back in February.
Better late than never.

Also, thank you to Nick Loman for a discussion in 2011 which
was one of the motivations in making this effort in the first place:

http://nickloman.github.io/high-throughput%20sequencing/2011/09/19/sambam-its-time-for-a-single-standard-for-assembly-output/

Also relevant are some of my blog posts from late 2011, with
screenshots illustrating SAM/BAM files with a padded or
un-padded reference:

http://blastedbio.blogspot.co.uk/2011/09/sambam-with-gapped-reference.html
http://blastedbio.blogspot.co.uk/2011/10/sambam-without-gapped-reference.html

If there are queries about the file format itself, please raise them
here on samtools-devel. I'm happy to receive comments about
the manuscript itself by email directly.

Thank you,

Peter

--
Peter Cock, Bioinformatician at the James Hutton Institute
http://www.hutton.ac.uk/staff/peter-cock