# nf-core/metatdenovo

#

[![GitHub Actions CI Status](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/metatdenovo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/metatdenovo/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/metatdenovo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10666590-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10666590) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1) [![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 Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/metatdenovo) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23metatdenovo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/metatdenovo)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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/metatdenovo** is a bioinformatics best-practice analysis pipeline for assembly and annotation of metatranscriptomic and metagenomic data from prokaryotes, eukaryotes or viruses. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/metatdenovo/results). ## Usage ![nf-core/metatdenovo metro map](docs/images/metat-metromap.png) 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) 3. Quality trimming and adapter removal for raw reads ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) 4. Optional: Filter sequences with [`BBduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) 5. Optional: Normalize the sequencing depth with [`BBnorm`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/) 6. Merge trimmed, pair-end reads ([`Seqtk`](https://github.com/lh3/seqtk)) 7. Choice of de novo assembly programs: 1. [`RNAspades`](https://cab.spbu.ru/software/rnaspades/) suggested for Eukaryote de novo assembly 2. [`Megahit`](https://github.com/voutcn/megahit) suggested for Prokaryote de novo assembly 8. Choice of orf caller: 1. [`TransDecoder`](https://github.com/TransDecoder/TransDecoder) suggested for Eukaryotes 2. [`Prokka`](https://github.com/tseemann/prokka) suggested for Prokaryotes 3. [`Prodigal`](https://github.com/hyattpd/Prodigal) suggested for Prokaryotes 9. Quantification of genes identified in assemblies: 1. Generate index of assembly ([`BBmap index`](https://sourceforge.net/projects/bbmap/)) 2. Mapping cleaned reads to the assembly for quantification ([`BBmap`](https://sourceforge.net/projects/bbmap/)) 3. Get raw counts per each gene present in the assembly ([`Featurecounts`](http://subread.sourceforge.net)) -> TSV table with collected featurecounts output 10. Functional annotation: 1. [`Eggnog`](https://github.com/eggnogdb/eggnog-mapper) -> Reformat TSV output "eggnog table" 2. [`KOfamscan`](https://github.com/takaram/kofam_scan) 3. [`HMMERsearch`](https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch) -> Ranking orfs based on HMMprofile with [`Hmmrank`](https://github.com/erikrikarddaniel/hmmrank) 11. Taxonomic annotation: 1. [`EUKulele`](https://github.com/AlexanderLabWHOI/EUKulele) -> Reformat TSV output "Reformat_tax.R" 2. [`CAT`](https://github.com/dutilh/CAT) 12. Summary statistics table. "Collect_stats.R" ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ``` | sample | fastq_1 | fastq_2 | -------- | ------------------------- | ------------------------- | | sample1 | ./data/S1_R1_001.fastq.gz | ./data/S1_R2_001.fastq.gz | | sample2 | ./data/S2_fw.fastq.gz | ./data/S2_rv.fastq.gz | | sample3 | ./S4x.fastq.gz | ./S4y.fastq.gz | | sample4 | ./a.fastq.gz | ./b.fastq.gz | ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired-end). Now, you can run the pipeline using: ```bash nextflow run nf-core/metatdenovo \ -profile \ --input samplesheet.csv \ --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](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/metatdenovo/usage) and the [parameter documentation](https://nf-co.re/metatdenovo/parameters). ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/metatdenovo/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/metatdenovo/output). > [!NOTE] > Tables in `summary_tables` directory under the output directory are made especially for further analysis in tools like R or Python. ## Credits nf-core/metatdenovo was originally written by Danilo Di Leo (@danilodileo), Emelie Nilsson (@emnilsson) & Daniel Lundin (@erikrikarddaniel). ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#metatdenovo` channel](https://nfcore.slack.com/channels/metatdenovo) (you can join with [this invite](https://nf-co.re/join/slack)). ## Citations If you use nf-core/metatdenovo for your analysis, please cite it using the following doi: [10.5281/zenodo.10666590](https://doi.org/10.5281/zenodo.10666590) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: > **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](https://dx.doi.org/10.1038/s41587-020-0439-x).

License
  MIT

## Contents

- ["nf-core/metatdenovo"]
- assets/
- conf/
- docs/
- docs/images/
- modules/
- modules/local/
- modules/nf-core/
- workflows/
- subworkflows/
- nextflow.config
- README.md
- nextflow_schema.json
- CHANGELOG.md
- LICENSE
- CODE_OF_CONDUCT.md
- CITATIONS.md
- modules.json
- docs/usage.md
- docs/output.md
- .nf-core.yml
- .pre-commit-config.yaml
- .prettierignore