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metagenomeassembly

https://github.com/sanger-tol/metagenomeassembly

Science Score: 65.0%

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 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization sanger-tol has institutional domain (www.sanger.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords

nextflow pipeline
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
Statistics
  • Stars: 2
  • Watchers: 5
  • Forks: 0
  • Open Issues: 15
  • Releases: 6
Topics
nextflow pipeline
Created almost 2 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

sanger-tol/metagenomeassembly

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Introduction

sanger-tol/metagenomeassembly is a bioinformatics pipeline for the assembly and binning of metagenomes using PacBio HiFi data and (optionally) Hi-C Illumina data.

sanger-tol/metagenomeassembly workflow diagram

Pipeline summary

  1. Assembles raw reads using metaMDBG.
  2. Maps HiFi and (optionally) Hi-C reads to the assembly using minimap2 and bwa-mem2.
  3. Bins the assembly using MetaBat2, MaxBin2, Bin3C (Hi-C binning), and Metator (Hi-C binning).
  4. (optionally) refine the bins using DAS_Tool and MagScoT.
  5. Assesses the completeness and contamination of bins using CheckM2 and assesses ncRNA content using tRNAscan-SE for tRNA and Infernal+Rfam for rRNA.
  6. Assigns taxonomy to bins using GTDB-TK and converts assignments to NCBI taxonomy labels.
  7. Summarises information at the bin level.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a YAML with your input data that looks as follows:

input.yaml:

yaml id: SampleName pacbio: fasta: - /path/to/pacbio/file1.fasta.gz - /path/to/pacbio/file2.fasta.gz - ... hic: cram: - /path/to/hic/hic1.cram - /path/to/hic/hic2.cram - ... enzymes: - enzyme_name_1 (e.g. DpnII) - enzyme_name_1 (e.g. HinfI) - ...

Now, you can run the pipeline using:

bash nextflow run sanger-tol/metagenomeassembly \ -profile <docker/singularity/.../institute> \ --input input.yaml \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/metagenomeassembly was originally written by Jim Downie, Will Eagles, Noah Gettle.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use sanger-tol/metagenomeassembly for your analysis, please cite it using the following doi: 10.5281/zenodo.15090769

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

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.

Owner

  • Name: Tree of Life programme
  • Login: sanger-tol
  • Kind: organization
  • Location: United Kingdom

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology

Citation (CITATION.cff) 

authors:
  - affiliation: Wellcome Sanger Institute
    email: jd42@sanger.ac.uk
    family-names: Downie
    given-names: Jim
    orcid: https://orcid.org/0000-0002-7175-0533
    website: https://github.com/prototaxites
  - affiliation: Wellcome Sanger Institute
    email: 84074349+weaglesBio@users.noreply.github.com
    family-names: Eagles
    given-names: Will
    orcid: https://orcid.org/0009-0006-9956-0404
    website: https://github.com/weaglesBio
  - affiliation: Wellcome Sanger Institute
    family-names: Gettle
    given-names: Noah
    orcid: https://orcid.org/0000-0003-3407-4086
    website: https://github.com/gettl008
cff-version: 1.2.0
commit: 03874666ebe537c1cf5b1b8d5afaa13b6639b152
date-released: "2025-04-11"
doi: 10.5281/zenodo.15090769
license: MIT
message: If you use this software, please cite it using the metadata from this file
  and all references from CITATIONS.md .
repository-code: https://github.com/sanger-tol/metagenomeassembly
title: sanger-tol/metagenomeassembly v1.1.0 - The Elfin Knight
type: software
url: https://pipelines.tol.sanger.ac.uk/metagenomeassembly
version: 1.1.1

GitHub Events

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Last synced: 8 months ago

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Top Authors
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  • prototaxites (7)
  • ThorstenHansen (1)
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Top Labels
Issue Labels
enhancement (5) Module (2) bug (2)
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Dependencies

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