recipe samestr

SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.

Homepage:

https://github.com/danielpodlesny/samestr/

Developer docs:

https://github.com/danielpodlesny/samestr

License:

AGPL / GNU Affero General Public License v3

Recipe:

/samestr/meta.yaml

Links:

doi: 10.1186/s40168-022-01251-w

package samestr

Versions:

1.2023.4-0,  1.2023.3-0

Depends:

• biopython 1.81

• blast >=2.6.0

• mafft 7.515

• muscle 3.8.1551

• numpy 1.24.2

• pandas 1.5.3

• pysam 0.20.0

• python >=3.9

• samtools 0.1.19

• scipy 1.10.0

Required By:

Installation

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

conda install samestr

and update with:

conda update samestr

or use the docker container:

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

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

Download stats

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