version 2.57

[Julian Catchen]

Hi All,

We have made a small Stacks release today -- 2.57. In this release we
fix a few internal bugs with respect to basepair coordinates in some
populations outputs (no changes to any data analysis).

To clarify how Stacks reports loci, and their internal SNPs and
haplotypes, with respect to their internal zero-based coordinates, and
their reference-aligned one-based coordinates, we added a new section to
the manual with lots of pictures to show precisely how to interpret SNPs
and DNA strands and haplotypes and their exact locations:

http://catchenlab.life.illinois.edu/stacks/manual/#coords

(*this was created by RADinitio guru, Angel Rivera-Colon).

A second small feature we added is for process_radtags. If you specify a
barcodes file with sample names in it, process_radtags will name your
demultiplexed output files according to the sample name you provide.
Now, if you supply the same sample name to multiple barcodes,
process_radtags will merge the output into a single file. So, if you
have multiplexed certain samples with multiple barcodes, the software
can merge them all together while demultiplexing. We have added some
examples of what these barcode files look like in the manual as well:

http://catchenlab.life.illinois.edu/stacks/manual/#specbc

Best wishes,

julian

[Giulia Trauzzi]

Hi Julian,

thanks for sharing this.

Would this version of stacks be available on bioconda?

Regards,

Giulia

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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