recipe tritimap

Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae.

Homepage:

https://github.com/fei0810/Triti-Map

Documentation:

https://github.com/fei0810/Triti-Map/wiki

License:

MIT

Recipe:

/tritimap/meta.yaml

Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae, which contains a suite of user-friendly computational packages and web-interface integrating multi-omics data from Triticeae species including genomic, epigenomic, evolutionary and homologous information.

Triti-Map could efficiently explore trait-related genes or functional elements not present in the reference genome and reduce the time and labor required for gene mapping in large genome species.

package tritimap

Versions:

0.9.7-0,  0.9.6-0,  0.9.5-0,  0.9.4-0,  0.9.3-0,  0.9.2-0,  0.9.1-0,  0.9.0-0

Depends:

• abyss 2.0.2.*

• bedops 2.4.39.*

• bioawk

• biopython

• blast >=2.5.0

• bwa 0.7.17.*

• bwa-mem2 2.2.1.*

• click >=7

• fastp >=0.20.1

• gatk4 >=4.2.0

• hmmer 3.3.2.*

• minimap2 >=2.17

• python 3.9.2.*

• r-base 4.0.2.*

• r-jsonlite 1.7.2.*

• r-qtlseqr 0.7.5.2.*

• samtools 1.12.*

• seqkit >=0.15.0

• snakemake >=6.0.3

• spades 3.15.0.*

• star 2.7.6a.*

• xmltramp2 3.1.1.*

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install tritimap

and update with:

conda update tritimap

or use the docker container:

docker pull quay.io/biocontainers/tritimap:<tag>

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

Download stats

Link to this page

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