- recipe reparation_blast
A pipeline that detects novel open reading frames with ribseq data for bacteria.
- Homepage:
- License:
GPL3
- Recipe:
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.
- package reparation_blast¶
-
- Versions:
1.0.9-3
,1.0.9-2
,1.0.9-1
,1.0.9-0
,1.0.8-0
,1.0.7-2
,1.0.7-0
,v1.0.7-1
,v1.0.7-0
,1.0.9-3
,1.0.9-2
,1.0.9-1
,1.0.9-0
,1.0.8-0
,1.0.7-2
,1.0.7-0
,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:
- Required By:
Installation
With an activated Bioconda channel (see 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
<tag>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/reparation_blast/README.html)