From cbef376627ff3dd4338591b1d55e945bc2134962 Mon Sep 17 00:00:00 2001 From: "Z.-L. Deng" Date: Thu, 8 Feb 2024 14:46:18 +0100 Subject: [PATCH] Update README.md update the readme for adapted mag workflow --- README.md | 27 +++++---------------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index c851487d..3943828f 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,8 @@ -# ![nf-core/mag](docs/images/nf-core-mag_logo_light.png#gh-light-mode-only) ![nf-core/mag](docs/images/nf-core-mag_logo_dark.png#gh-dark-mode-only) - -[![GitHub Actions CI Status](https://github.com/nf-core/mag/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/mag/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8)](https://doi.org/10.5281/zenodo.3589527) -[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007) - -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) -[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) -[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/mag) - -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) - ## Introduction -**nf-core/mag** is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes. +This pipeline is a modified version of the renowned nf-core/mag workflow, meticulously refined to incorporate best practice tools recognized for their performance in the CAMI2 benchmark. In an effort to broaden the utility and applicability of the workflow, we have integrated support specifically for long reads data, incorporating the advanced long-read assembler [Flye](https://github.com/fenderglass/Flye) alongside the high-performing short-read assembler [MetaHipMer](https://bitbucket.org/berkeleylab/mhm2/src/master/). Moreover, the workflow now incorporates additional highly performant metagenome binners and bin refinement tools, including [MetaBinner](https://github.com/ziyewang/MetaBinner), [UltraBinner](https://github.com/Huangpq2019/UltraBinner), and [MetaWRAP](https://github.com/bxlab/metaWRAP). + -

- nf-core/mag workflow overview -

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! @@ -31,11 +14,11 @@ By default, the pipeline currently performs the following: it supports both shor The pipeline then: - assigns taxonomy to reads using [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [Kraken2](https://github.com/DerrickWood/kraken2/wiki) -- performs assembly using [MEGAHIT](https://github.com/voutcn/megahit) and [SPAdes](http://cab.spbu.ru/software/spades/), and checks their quality using [Quast](http://quast.sourceforge.net/quast) +- performs assembly using [MEGAHIT](https://github.com/voutcn/megahit), [MetaHipMer](https://bitbucket.org/berkeleylab/mhm2/src/master/), [SPAdes](http://cab.spbu.ru/software/spades/), long reads assembler [Flye](https://github.com/fenderglass/Flye) and checks their quality using [Quast](http://quast.sourceforge.net/quast). - (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html) - predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal) -- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), or [CheckM](https://ecogenomics.github.io/CheckM/), and optionally [GUNC](https://grp-bork.embl-community.io/gunc/). -- optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool) +- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), [MetaBinner](https://github.com/ziyewang/MetaBinner) and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), or [CheckM](https://ecogenomics.github.io/CheckM/), and optionally [GUNC](https://grp-bork.embl-community.io/gunc/). +- optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool), [UltraBinner](https://github.com/Huangpq2019/UltraBinner) and [MetaWRAP](https://github.com/bxlab/metaWRAP) - assigns taxonomy to bins using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk) and/or [CAT](https://github.com/dutilh/CAT) Furthermore, the pipeline creates various reports in the results directory specified, including a [MultiQC](https://multiqc.info/) report summarizing some of the findings and software versions.