CRISPRroots v.1.3

CRISPRroots v.1.3 is finally ready!

The major improvement over v.1.2 is that in this new version of the software we abandon the usage of conda environments in favor of docker/singularity. This is because conda environments are not stable over time (eg. if an environment build is removed or replaced) and we ended up getting new errors over time which forced us to re-define the environments. The docker/singularity, instead, is fixed and does not require any new installation: it is downloaded as a self-contained system from DockerHub and includes all the software required to run CRISPRroots.

Additionally, we have included new columns in the report files:

the complete gRNA-DNA binding patterns (including the parts of the binding that are not used to make the hybrid with lowest MFE)

the allelic depths that support a variant for the variant-based analysis

In this version we terminate the support of eSNPKaryotyping, which so far was an optional part of the pipeline. We have never used the results of this tool (not even in the original publication of CRISPRroots) because they do not look convincing, and the plots often come out wrong (with missing chromosomes due to shifts). The tool is poorly written, and requires manual code changes when one selects a different genome.

CRISPRroots v1.2

Updates for CRISPRroots v1.2

CRISPRroots v1.1

Updates for CRISPRroots v1.1 for resubmission

v1.0

Pre release of crisprroots