[Biopython] Fwd: [mira_talk] new sff_extract

[Peter Cock]

Apologies if this arrives twice, the OBF mail server was
down earlier today - more news about that tomorrow
I hope, along with information about the website.
(This email is partly to confirm the list are alive again.)

Peter

---------- Forwarded message ----------
From: *Peter Cock*
Date: Wednesday, October 31, 2012
Subject: [mira_talk] new sff_extract
To: Biopython Mailing List <biopython at lists.open-bio.org>


Hi all,

For those working with SFF files (from Roche or IonTorrent),
Jose's sff_extract tool has often been a popular alternative
to the Roche (Linux only) off instrument applications - and
Biopython's SFF support was based on sff_extract (thanks
again Jose!).

Jose has just announced (on the MIRA assembler mailing
list) a new version of sff_extract which now calls the
Biopython SFF code for the low level binary file access,
and comes with some additional related tools.

See below for details, original thread archive here:
http://www.freelists.org/post/mira_talk/new-sff-extract

Peter

---------- Forwarded message ----------
From: Jose Blanca <jblanca at upv.es <javascript:;>>
Date: Wed, Oct 31, 2012 at 9:39 AM
Subject: [mira_talk] new sff_extract
To: "mira_talk at freelists.org <javascript:;>"
<mira_talk at freelists.org<javascript:;>
>


Hi:

Sometime ago we discussed in this list the future of sff_extract. We
started working on it and we have a version that we think is working.
The sff_extract functionality has been split in two sff_extract and
split_matepairs that can be linked together with a pipe. We haven't
done extensive testing so if you use them, please let us know.
These utilities are bundled with some other little tools that we have
developed for our day to day work. They are all written in python and
they use biopython.
You can take a look at the development site:

https://github.com/JoseBlanca/seq_crumbs

Or our site:

http://bioinf.comav.upv.es/seq_crumbs/

Of course we'd love to have some feedback.
Best regards,

--
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)

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