recipe reparation_blast

A pipeline that detects novel open reading frames with ribseq data for bacteria.

Homepage

https://github.com/RickGelhausen/REPARATION_blast

License

GPL3

Recipe

/reparation_blast/meta.yaml

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

1.0.9-1,  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, 

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

• biopython 1.77.*

• blast

• glimmer

• openssl

• perl >=5.26.2,<5.26.3.0a0

• perl-bioperl >=1.7.2

• perl-posix

• plastid

• prodigal

• pysam 0.16.0.1.*

• r-ggplot2

• r-prroc

• r-randomforest

• r-rocr

• r-sizer

• samtools

Required By

Installation

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 <tag>)

Link to this page

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