magpurify2


Namemagpurify2 JSON
Version 1.0.2 PyPI version JSON
download
home_pagehttps://github.com/apcamargo/magpurify2/
SummaryIdentify and remove contaminants from metagenome-assembled genomes.
upload_time2023-05-16 02:58:08
maintainer
docs_urlNone
authorAntonio Camargo
requires_python>=3.6
licenseGNU General Public License v3.0
keywords bioinformatics metagenomics metagenome-assembled genomes
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            <img src="https://raw.githubusercontent.com/apcamargo/magpurify2/master/website/.vuepress/public/logo_without_type.svg?token=AFPA2JEOQW3DH6XWN62XPGC6YH3HQ" align="left" width="200" height="150px"/>
<img align="left" width="0" height="150px" hspace="0"/>

Improve the quality of metagenome-assembled genomes by identifying and removing contaminant sequences with an easy-to-use and modular command-line interface.

[![MIT License](https://img.shields.io/badge/license-MIT-007EC7.svg?style=flat-square)](/LICENSE) [![Fish Shell Version](https://img.shields.io/badge/fish-≥v2.2.0-007EC7.svg?style=flat-square)](http://fishshell.com) [![Travis Build Status](http://img.shields.io/travis/oh-my-fish/oh-my-fish.svg?style=flat-square)](https://travis-ci.org/oh-my-fish/oh-my-fish)

You can find MAGpurify2's full documentation at its [website](https://apcamargo.github.io/magpurify2/).

---

## Quick start


Download test data:

```bash
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:

```bash
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:

```bash
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
```

Raw data

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Antonio Camargo
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