CracTools

Integrated pipelines for RNA-Seq analysis using CRAC (mapping tool) additional fields.
Find more about CracTools's concept here.

What's new?

CracTools-core version 1.24 released


The new version of CracTools-core has been released. Is it available in CPAN or as a tarball.

This version includes some bugs corrections in the variant calling output deliverd by cractools extract command (invalid headers and bad reference nucleotid on SNPs).


CracTools-core version 1.22 released


The new version of CracTools-core has been released. Is it available in CPAN or as a tarball.

This version includes some bugs corrections in the variant calling from cractools extract command (VCF output). It is also compliant with the new version of CRAC that has corrected some issues with variant positions.

Please consider re-run your analysis for variant detection purposes with the latest CRAC and CracTools versions.


CracTools-core version 1.21 released


The new version of CracTools-core has been released. Is it available in CPAN or as a tarball.

It includes bugs correction in the cractools extract command and now provides full VCF format compatibility with IGV genomic browser.


CracTools-core version 1.2 released


The new version of CracTools-core has been released. Is it available in CPAN or as a tarball.

It comes with a new datastructure: CracTools::GenomeMask, wich defines a bitset over a whole genome and enable fast nucleotide labelling.

It also provide command line tools (under the cractools binary) like cractools extract that is a simple extracting tool that collapse biological events (SNVs, Indels, Splice junctions, Chimeras) identified by CRAC at the read scale and generate standard NGS variant files (VCF, BED).

CracTools-core 1.2 is also more stable (bug corrections in CracTools::Annotator) and more documentated.


Publication of digitagCT


The publication on digitagCT has been accepted for publication in Nucleic Acids Research :

Nicolas Philippe, Elias Bou Samra, Anthony Boureux, Alban Mancheron, Florence Rufflé, Qiang Bai, John De Vos, Eric Rivals and Thérèse Commes, Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. doi: 10.1093/nar/gkt1300


subscribe via RSS

News and updates

New releases and related tools will be announced through the CracTools mailing list.

Getting started

You want to try the CracTools? Download it and check our getting started guide.

Contact us

Any question regarding the software? Send an email to cractools-bugs@lists.gforge.inria.fr.

Publications

Nicolas Philippe, Elias Bou Samra, Anthony Boureux, Alban Mancheron, Florence Rufflé, Qiang Bai, John De Vos, Eric Rivals and Thérèse Commes. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome doi: 10.1093/nar/gkt1300