Seal / News: Recent posts

new release: Seal-0.3.2

Another incremental release on the 0.3 branch.

Only Seqal is modified by this release. We have enabled the Smith-Waterman alignment of unmapped reads with mapped mates. With this latest improvement Seqal produces alignments that are pretty much identical to BWA 0.5.10.

We have just compared Seqal to BWA with a much bigger dataset than the one used for the publication. Out of approximately 63 million paired reads, only 0.00031% presented any alignment difference (195, to be precise). The differences were due to reads that only Seqal or only BWA were able to align (about half and half); we suspect the difference may be due to randomness used to generate gaps in the reference or to break ties in the alignment process. Incidentally, aligning the same dataset with the same version of BWA, then reordering the reads and realigning it produced ~1500 different alignments.... read more

Posted by Luca Pireddu 2013-02-07 Labels: new_release

new release: Seal-0.3.1 -- important!

Release 0.3.1 is an important bugfix release. If you're using Seal Seqal, you should upgrade immediately.

Last week we found a problem in the duplicates identification part of Seqal causing it to miss a significant portion of duplicate reads. If you're using Seqal to identify duplicates you are urged to upgrade and you should check your data.

Version 0.3.1 solves this problem. Our latest comparison with Picard finds that the results are equivalent to within 1e-7 of the number of duplicates (e.g. 8 / 8 000 000 duplicates) and about 1e-8 in the total number of reads. There is still a rare corner case where the two tools produce different results, but we're still investigating that issue.

Posted by Luca Pireddu 2012-02-29

new release: Seal-0.3.0

We've just released a new version of Seal: 0.3.0!

We have a number of new items in this release:

  • new program, RecabTable, to calculate empirical base quality recalibration tables;
  • fastq input, in particular the fastq files with meta-data produced by Casava 1.8;
  • TsvSort: a distributed text sorting utility;
  • Bug fixes and usability improvements.

If you're updating from an older release, please read the "News" section in the documentation.... read more

Posted by Luca Pireddu 2012-01-27

The Seal project will be switching to git

Hello all. We have decided to switch the Seal repository from Bazaar to git. Nothing against Bazaar, but we're trying to standardize our projects to one version control tool, and git found the most agreement with all our collaborators.

We hope this doesn't cause problems to anyone who may have checked out the Seal repository.

We don't have an exact timeline but it will happen soon. Cheers.

Posted by Luca Pireddu 2011-11-22

new release: Seal-0.2.3

We're release-happy at this time of the year!

Following the recent release of version 0.2.2, the fellows at our sequencing facility had a couple of requests concerning the merge_alignments utility which we implemented quickly and wrapped into this release:

  • Reference checksums
  • additional SAM header tags

See the documentation for details: http://biodoop-seal.sourceforge.net/news.html

Enjoy!

Posted by Luca Pireddu 2011-09-13

new release: Seal-0.2.2

This release mainly improves usability, with changes such as:
all programs have the same interface
support for configuration files for preset properties

For a full list of changes see the summary in the documentation:
http://biodoop-seal.sourceforge.net/news.html

Enjoy!

Posted by Luca Pireddu 2011-09-08

new release: Seal-0.2.1

Bug fix release.

Fixes alternate alignments reported by Seqal with the XA tag. Previous version wrongly reported the main alignment's chr instead of the correct alternate alignment.

Posted by Luca Pireddu 2011-07-11

new release: Seal-0.2.0

We've just released version 0.2.0 of the Seal suite. Since the previous release, the main additions are:

  • sequence demultiplexing tool (Demux)
  • improved installation procedure
  • an example sequencing workflow using Seal
  • various other small improvements and bug fixes

Enjoy!

Posted by Luca Pireddu 2011-06-29

first release: Seal-0.1.0!

We've just released Seal 0.1.0, the first official release for this project. This version is being used at the CRS4 Sequencing and Genotyping Platform to process the output of their DNA sequencing runs.

We look forward to your feedback! Let us know if you have any problems installing or using the software.

Posted by Luca Pireddu 2011-05-09

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