Identify and remove contaminants from metagenome-assembled genomes.
Project description
Improve the quality of metagenome-assembled genomes by identifying and removing contaminant sequences with an easy-to-use and modular command-line interface.
You can find MAGpurify2's full documentation at its website.
Quick start
Download test data:
fileId="1-Gf-FsVIcARqrUb-LHS_FZlb-sCGAmfo"
fileName="magpurify2_test_data.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2_test_data.tar.gz
Download database:
fileId="1ooWiR3LplBy5GsY5wZ7o6dwswiCWVvmi"
fileName="magpurify2DB.v1.0.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2DB.v1.0.tar.gz
Execute the pipeline:
magpurify2 composition test_data/genomes/* output
magpurify2 coverage test_data/genomes/* output --bam_files test_data/bam_files/*
magpurify2 taxonomy test_data/genomes/* output magpurify2DB
magpurify2 filter test_data/genomes/* output filtered_genomes
Project details
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