thackl / mbc Goto Github PK

# download workflow
git clone https://github.com/thackl/mbc
cd mcb

# install dependencies via conda or mamba (https://github.com/conda-forge/miniforge)
mamba create -n 
mamba activate mbc
mamba env update --file env.yaml

# run mbc
Usage:
./mbc -h                                      # show help
./mbc [options] -m marker <sample.fx> ...
./mbc [options] [-m marker] -t samples.tsv
./mbc [options] --setup-databases             # NOT YET WORKING!!!

samples.tsv

tab-separted table with info on each sample. The header is required. Paths to

files can be relative to sample.tsv or absolute. For example:

#file	marker	min_length	max_length
../fungi.fq	ITS	2000	2500
/dat/bee.fa	COI	600	800

marker

Currently supported are combination of SSU:ITS:LSU, or COI. A single marker/combination is applied to all input files. Different markers for each input file need to be separated by “,”. Supersedes markers listed in samples.tsv.

See Advanced database setup for alternatives and customization of databases.

See Known issues and https://github.com/thackl/mbc/issues for questions, problems or feedback.

The pipeline produces the following final files in results/:

<sample_id>_classified.tsv

tab-separated file with one line per classified query with the fields: query_id, query_tophit_identity, query_tophit_coverage, query_tophits_consensus_lineage

TODO

If you need databases in a different location you can adjust db_dir in config.yaml to whatever suits your system.

If you prefer to handle downloads manually or use existing files, copy any file you don’t want mbc to download automatically into databases/ (or the respective config.yaml/db_dir) before running --setup-databases.

Note though, unless you add --notemp to the --snake-arguments, all but the final diamond-formatted database files will be deleted from databases/ at the end of the setup phase.

cd databases/

# Latest RVDB
url=https://rvdb-prot.pasteur.fr/ && 
db=$(curl -fs $url | grep -oPm1 'files/U-RVDBv[0-9.]+-prot.fasta.xz')
curl $url/$db -o rvdb100.faa.xz

# UniRef50
wget https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz

# NCBI taxonomy stuff
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -xzf taxdump.tar.gz nodes.dmp names.dmp

None known