recipe reparation_blast

a pipeline that uses ribosome profiling data for a de novo open reading frame delineation in prokaryotic (bacterial) genomes. I changed the original reparation project to use the open-source blast tool ( instead of the commercial usearch –ublast tool ( I did this in order to add this tool to bioconda without having licensing issues with the commercial usearch -ublast tool. The original software was created at VIB-UGent Center for Medical Biotechnology and Lab of Bioinformatics and Computational Genomics (Biobix), University of Gent, Belgium, by Elvis Ndah. ( Be advised that the adapted version has slightly different results and is slower than the original reparation software.






package reparation_blast

(downloads) docker_reparation_blast


v1.0.7-1, v1.0.7-0, v1.0.6-0, v1.0.5-0, v1.0.4-0, v1.0.3-2, v1.0.2-1, v1.0.1-0

Depends blast


Depends glimmer

Depends perl


Depends perl-bioperl


Depends perl-posix

Depends plastid

Depends prodigal

Depends pysam


Depends r-ggplot2


Depends r-prroc


Depends r-randomforest

Depends r-rocr

Depends r-sizer

Depends samtools



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install reparation_blast

and update with:

conda update reparation_blast

or use the docker container:

docker pull<tag>

(see reparation_blast/tags for valid values for <tag>)