What's new?

CRAC 1.5.0 released

Version 1.5.0 of CRAC is released. The main changes are the following ones:

  • Some bugs fixed llike inter compiler consistency, run with large reads file and bugs #16581, #16807, #16931, #17175 have been fixed.
  • Update SAM specification in order to be consistent with the last SAM version consistency (including chimeric aligments, extended fields, etc).
  • Display multiple alignments in SAM file for perfect hits.
  • Add an optional ProgressBar in order to check the progression of CRAC in batch mode.
  • Update the documentation, the sam specification and the man page.

 

   

CRAC 1.3.2 released

Version 1.3.2 of CRAC is released. The main changes are the following ones:

  • Bug corrections affecting very large files in GkArrays (thanks a lot to Caroline Menguy for her help): processing very large files could take too many time (or even never finish).
  • A new option --treat-multiple has been added that allows to have information on all the reads in SAM file (by default CRAC doesn't care about reads that seem to appear too many times).
  • Output can be written on STDOUT using -o - and the summary can be written in a specific file using --summary.
  • Option --max-paired-length has been removed since its use is the same as for --max-splice-length. Please use the latter instead.
  • Few minor corrections (thanks to zhouwp for pointing out a problem with old version of grep, with make check).
   

Tags : crac release

See you at JOBIM and GCC

CRAC has a poster at the Galaxy Community Conference in Oslo, Norway. CRAC was also presented today at the french JOBIM conference. You can see the slides here.

   

Tags : crac poster slide conference

CRAC mentioned in Nature

Nature wrote about CRAC in the  Research Highlights section of its May 2 issue.

Just a tiny mistake: all the authors are not from Montpellier and are not part of Eric's team ;)

   

CRAC version 1.3.0 released

A new version of CRAC is released.

Among the main changes:

  • SAM format is now compliant with Picard tools
  • CRAC is now able to produce gzip-compressed output files (use --gz option) — thanks to Linlin Yan for asking
  • CRAC is now built with libraries embedded by default (thanks to Sarah Pohl for pointing that out)
  • Several bugs have been fixed regarding problems related to CIGAR string in SAM output (thanks to Linlin Yan for reporting one of them).
   

CRAC version 1.2.4 released

CRAC is now released under version 1.2.4. It integrates several improvements:

Bug corrections :

  • Bug #15605 solved (segfault on very specific read), on both strands
  • Bug #15630 corrected: range in the BWT was not properly initialized with revcomp
  • FM-Index: Bug solved with genome length multiple of 64.
  • Update headers for paired-end-chimera crac homemade file.
  • Correct several bugs in CRAC emt :
    • Fix multi-threading
    • Added FASTA support

News

  • CRAC is now using gkArrays 2.0.3
  • New algorithm for chimera validation using paired-end reads.
    We had miss some cases in the process of validating chimera junctions with paired-end reads.
  • Add unit tests in CRAC :
    Every bug solved is now included as a unit test to avoid regression.
  • Add XR field in SAM output for information relative to the read (p_loc and p_support are now under the XR field

This changes were made by Jérôme Audoux, Nicolas Philippe and Mikaël Salson (in alphabetical order).

   

CRAC version 1.2.3 released

CRAC is now released under version 1.2.3. It integrates several improvements:

Correction of several bugs:

  • Correct --all argument. No paired-end-chimera is created if we are not using paired-end reads
  • Bug #15605 corrected (segmentation fault in FM-index, when a range was at the top of the BWT, but then becomes empty)
  • Deletion position was indicated one position before where it should be
  • Correct the k-mer verification test in stringent-chimera. The test to determine if the kmer used for verification wasn't in a break was based on support profile instead of location profile.

Add several improvements:

  • Add some unit tests 
  • Use version 2.0.2 of Gk-arrays

This changes were made by Jérôme Audoux, Nicolas Philippe and Mikaël Salson (in alphabetical order).

   

Galaxy wrapper released

Galaxy is « an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses ».

Marine Rohmer worked during her Master's on creating a Galaxy wrapper for CRAC. You can download it here. You may have to modify it to adapt it to your needs.

   

Tags : galaxy wrapper