A pipeline that detects novel open reading frames with ribseq data for bacteria.
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 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) instead of the commercial usearch --ublast tool (https://drive5.com/usearch/manual/ublast_algo.html). 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. (https://github.com/Biobix/REPARATION). Be advised that the adapted version has slightly different results and is slower than the original reparation software.
- Required By
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 quay.io/biocontainers/reparation_blast:<tag>
(see reparation_blast/tags for valid values for