recipe bmtagger

BMTagger aka Best Match Tagger is for removing human reads from metagenomics datasets

Homepage

ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/

License

Public Domain

Recipe

/bmtagger/meta.yaml

package bmtagger

Versions

3.101-5, 3.101-4, 3.101-3, 3.101-1

Depends

• blast

• bmfilter

• bmtool

• extract_fullseq

• gnu-getopt

• srprism

Required By

• kneaddata

• metawrap

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bmtagger

and update with:

conda update bmtagger

or use the docker container:

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

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

Notes

You may find it necessary to create a bmtagger.conf file to specify paired or single-end searching. The file should contain the line ‘srprismopts=”-b 100000000 -n 5 -R 0 -r 1 -M 7168”’ along with ‘-p true’ or ‘-p false’ for paired, and single, respectively. This config file can be passed to bmtagger.sh via the ‘-C’ option.

Link to this page

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