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autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes

https://github.com/kwanlab/autometa

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary

Keywords

binning metagenomics taxon-profiling
Last synced: 6 months ago · JSON representation ·

Repository

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes

Basic Info
Statistics
  • Stars: 41
  • Watchers: 3
  • Forks: 15
  • Open Issues: 40
  • Releases: 13
Topics
binning metagenomics taxon-profiling
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Codeowners

README.md

Autometa

GitHub tag (latest SemVer)

An automated binning pipeline for single metagenomes, in particular host-associated and highly complex ones. Autometa is copyright 2020 Ian J. Miller, Evan Rees, Izaak Miller and Jason C. Kwan, and is released under the GNU Affero General Public License v3 (see LICENSE.txt). If you find Autometa useful to your work, please cite:

Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research, 2019. DOI: https://doi.org/10.1093/nar/gkz148

Documentation

Documentation Status

Full documentation is hosted on autometa.readthedocs.io

Quickstart

:shell: Bash workflow

install with bioconda Conda

1. Setup env

Install into your current env...

bash mamba install -c conda-forge -c bioconda autometa

... or create a new env

bash mamba create -n autometa -c conda-forge -c bioconda autometa

2. Download the bash workflow template, autometa.sh

3. Edit the input parameters

4. Run the workflow

:green_apple: Nextflow Workflow

Nextflow

1. Setup env

:student: This workflow requires only nextflow and nf-core be installed.

Install into your current env...

bash mamba env update -n <your-env> --file=https://raw.githubusercontent.com/KwanLab/Autometa/main/nextflow-env.yml

... or create a new env

```bash mamba env create --file=https://raw.githubusercontent.com/KwanLab/Autometa/main/nextflow-env.yml

Activate the env after creation

mamba activate autometa-nf ```

2. Launch and run the workflow

bash nf-core launch KwanLab/Autometa

For developers

Contributing Guidelines GitHub good first issues

GitHub language count GitHub top language codecov

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. In addition, references of tools and data used in this pipeline are as follows:

Owner

  • Name: KwanLab
  • Login: KwanLab
  • Kind: organization

https://twitter.com/kwan_lab

Citation (CITATION.cff) 

cff-version: 1.2.0
message: 'If you use this software, please cite it as below.'
title: Autometa
preferred-citation:  
  type: article
  authors:
  - given-names: Ian J.
    family-names: Miller
  - given-names: Evan R.
    family-names: Rees
  - given-names: Jennifer
    family-names: Ross
  - given-names: Izaak
    family-names: Miller
  - given-names: Jared
    family-names: Baxa
  - given-names: Juan
    family-names: Lopera
  - given-names: Robert L.
    family-names: Kerby
  - given-names: Federico E.
    family-names: Rey
  - given-names: Jason C.
    family-names: Kwan
  orcid: 'https://orcid.org/0000-0001-9933-1536'
  title: 'Autometa: automated extraction of microbial genomes from individual shotgun metagenomes'
  year: 2019
  journal: Nucleic Acids Research
  volume: 47
  issue: 10  
  url: 'https://github.com/KwanLab/Autometa'
  doi: 10.1093/nar/gkz148

GitHub Events

Total
  • Issues event: 1
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 32
  • Push event: 37
  • Pull request review event: 2
  • Pull request event: 8
  • Create event: 4
Last Year
  • Issues event: 1
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 32
  • Push event: 37
  • Pull request review event: 2
  • Pull request event: 8
  • Create event: 4

Dependencies

docs/requirements.txt pypi
  • readthedocs-sphinx-search ==0.1.1
  • sphinx ==4.2.0
  • sphinx_rtd_theme ==1.0.0
.github/workflows/docker_autometa.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
.github/workflows/docker_get_genomes_for_mock.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
.github/workflows/docker_mock_data_reporter.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • actions/upload-artifact v2 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/pytest_codecov.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2 composite
Dockerfile docker
  • continuumio/miniconda3 latest build
modules/nf-core/modules/bowtie2/align/meta.yml cpan
modules/nf-core/modules/prodigal/meta.yml cpan
setup.py pypi
tests/environment.yml conda
  • attrs
  • bedtools
  • biopython
  • black 22.3.0
  • bowtie2
  • diamond >=2.0
  • gdown
  • hmmer
  • numba >=0.47
  • numpy >=1.13
  • pandas >=1.1
  • parallel
  • pip
  • pre_commit
  • prodigal
  • pytest
  • pytest-cov
  • pytest-html
  • pytest-repeat
  • pytest-variables
  • python-annoy >=1.11
  • requests
  • rsync
  • samtools >=1.11
  • scikit-bio
  • scikit-learn >=1.3
  • scipy
  • sphinx
  • sphinx_rtd_theme
  • tqdm
  • trimap
  • tsne
  • umap-learn >=0.5