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viralmetagenome

Detect iSNV and construct whole viral genomes from metagenomic samples

https://github.com/nf-core/viralmetagenome

Science Score: 67.0%

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

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    CITATION.cff file
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    Found 10 DOI reference(s) in README
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    Links to: ncbi.nlm.nih.gov
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    Low similarity (9.1%) to scientific vocabulary

Keywords

epidemiology fastq nextflow nf-core ngs pipeline viral-metagenomics virology virus-genomes workflow
Last synced: 6 months ago · JSON representation ·

Repository

Detect iSNV and construct whole viral genomes from metagenomic samples

Basic Info
Statistics
  • Stars: 22
  • Watchers: 3
  • Forks: 3
  • Open Issues: 14
  • Releases: 2
Topics
epidemiology fastq nextflow nf-core ngs pipeline viral-metagenomics virology virus-genomes workflow
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/viralmetagenome

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

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Introduction

Viralmetagenome is a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.

viralmetagenome-workflow

  1. Read QC (FastQC)
  2. Performs optional read pre-processing
  3. Metagenomic diversity mapping
    • Performs taxonomic classification and/or profiling using one or more of:
    • Plotting Kraken2 and Kaiju (Krona)
  4. Denovo assembly (SPAdes, TRINITY, megahit), combine contigs.
  5. [Optional] extend the contigs with sspace_basic and filter with prinseq++
  6. [Optional] Map reads to contigs for coverage estimation (BowTie2,BWAmem2 and BWA)
  7. Contig reference idententification (blastn)
    • Identify top 5 blast hits
    • Merge blast hit and all contigs of a sample
  8. [Optional] Precluster contigs based on taxonomy
    • Identify taxonomy Kraken2 and\or Kaiju
    • Resolve potential inconsistencies in taxonomy & taxon filtering | simplification bin/extract_precluster.py
  9. Cluster contigs (or every taxonomic bin) of samples, options are:
  10. [Optional] Remove clusters with low read coverage. bin/extract_clusters.py
  11. Scaffolding of contigs to centroid (Minimap2, iVar-consensus)
  12. [Optional] Annotate 0-depth regions with external reference bin/nocov_to_reference.py.
  13. [Optional] Select best reference from --mapping_constraints:
  14. Mapping filtered reads to supercontig and mapping constraints(BowTie2,BWAmem2 and BWA)
  15. [Optional] Deduplicate reads (Picard or if UMI's are used UMI-tools)
  16. Variant calling and filtering (BCFTools,iVar)
  17. Create consensus genome (BCFTools,iVar)
  18. Repeat step 14-17 multiple times for the denovo contig route
  19. [Optional] Variant annotation (SnpEff,SnpSift)
  20. [Optional] Consensus evaluation and annotation:
  21. Result summary visualisation for raw read, alignment, assembly, variant calling and consensus calling results (MultiQC)

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 samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2 sample1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz sample2,AEG588A5_S5_L003_R1_001.fastq.gz, sample3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.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/viralmetagenome \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --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.

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/viralmetagenome was originally written by Joon Klaps, Philippe Lemey, Liana Kafetzopoulou.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #viralmetagenome channel (you can join with this invite).

Citations

[!WARNING] Viralmetagenome is currently not Published. Please cite as: Klaps J, Lemey P, Kafetzopoulou L. Viralmetagenome: A metagenomics analysis pipeline for eukaryotic viruses. Github https://github.com/nf-core/viralmetagenome

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

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: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/viralmetagenome: Citations

# Citations

## [Viralmetagenome](https://github.com/nf-core/viralmetagenome)

!!! warning
Viralmetagenome is currently not Published. Please cite as:

    - Klaps J, Lemey P, Kafetzopoulou L. Viralmetagenome: A metagenomics analysis pipeline for eukaryotic viruses. __Github__ https://github.com/nf-core/viralmetagenome

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [Bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)

  > Bushnell B. (2022) BBMap, URL: http://sourceforge.net/projects/bbmap/

- [BCFtools](https://pubmed.ncbi.nlm.nih.gov/33590861/)

  > Danecek, Petr et al. “Twelve years of SAMtools and BCFtools.” GigaScience vol. 10,2 (2021): giab008. doi:10.1093/gigascience/giab008

- [blast](https://pubmed.ncbi.nlm.nih.gov/20003500/)

  > Camacho, Christiam et al. “BLAST+: architecture and applications.” BMC bioinformatics vol. 10 421. 15 Dec. 2009, doi:10.1186/1471-2105-10-421

- [Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

  > Langmead, Ben, and Steven L Salzberg. “Fast gapped-read alignment with Bowtie 2.” Nature methods vol. 9,4 357-9. 4 Mar. 2012, doi:10.1038/nmeth.1923

- [BWA-MEM](https://github.com/lh3/bwa)

  > Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2.

- [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2)

  > M. Vasimuddin, S. Misra, H. Li and S. Aluru, "Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems," 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil, 2019, pp. 314-324, doi: 10.1109/IPDPS.2019.00041.

- [cdhit](https://pubmed.ncbi.nlm.nih.gov/23060610/)

  > Fu, Limin et al. “CD-HIT: accelerated for clustering the next-generation sequencing data.” Bioinformatics (Oxford, England) vol. 28,23 (2012): 3150-2. doi:10.1093/bioinformatics/bts565

- [checkv](https://pubmed.ncbi.nlm.nih.gov/33349699/)

  > Nayfach, Stephen et al. “CheckV assesses the quality and completeness of metagenome-assembled viral genomes.” Nature biotechnology vol. 39,5 (2021): 578-585. doi:10.1038/s41587-020-00774-7

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [fastp](https://github.com/OpenGene/fastp)

  > Chen, Shifu et al. “fastp: an ultra-fast all-in-one FASTQ preprocessor.” Bioinformatics (Oxford, England) vol. 34,17 (2018): i884-i890. doi:10.1093/bioinformatics/bty560

- [HUMID](https://humid.readthedocs.io/en/latest/usage.html)

  > Laros J, van den Berg R, **Github** https://github.com/jfjlaros/HUMID

- [iVar](https://www.ncbi.nlm.nih.gov/pubmed/30621750/)

  > Grubaugh, Nathan D et al. “An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.” Genome biology vol. 20,1 8. 8 Jan. 2019, doi:10.1186/s13059-018-1618-7

- [Kaiju](https://pubmed.ncbi.nlm.nih.gov/27071849/)

  > Menzel, Peter et al. “Fast and sensitive taxonomic classification for metagenomics with Kaiju.” Nature communications vol. 7 11257. 13 Apr. 2016, doi:10.1038/ncomms11257

- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)

  > Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.

- [leiden-algorithm](https://pubmed.ncbi.nlm.nih.gov/30914743/)

  > Traag, V A et al. “From Louvain to Leiden: guaranteeing well-connected communities.” Scientific reports vol. 9,1 5233. 26 Mar. 2019, doi:10.1038/s41598-019-41695-z

- [Mash](https://pubmed.ncbi.nlm.nih.gov/27323842/)

  > Ondov, Brian D et al. “Mash: fast genome and metagenome distance estimation using MinHash.” Genome biology vol. 17,1 132. 20 Jun. 2016, doi:10.1186/s13059-016-0997-x

- [Megahit](https://pubmed.ncbi.nlm.nih.gov/27012178/)

  > Li, Dinghua et al. “MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.” Methods (San Diego, Calif.) vol. 102 (2016): 3-11. doi:10.1016/j.ymeth.2016.02.020

- [Minimap2](https://pubmed.ncbi.nlm.nih.gov/29750242/)

  > Li, Heng. “Minimap2: pairwise alignment for nucleotide sequences.” Bioinformatics (Oxford, England) vol. 34,18 (2018): 3094-3100. doi:10.1093/bioinformatics/bty191

- [MMseqs2](https://pubmed.ncbi.nlm.nih.gov/29035372/)

  > Steinegger, Martin, and Johannes Söding. “MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.” Nature biotechnology vol. 35,11 (2017): 1026-1028. doi:10.1038/nbt.3988

- [Mosdepth](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030888/)

  > Pedersen, Brent S, and Aaron R Quinlan. “Mosdepth: quick coverage calculation for genomes and exomes.” Bioinformatics (Oxford, England) vol. 34,5 (2018): 867-868. doi:10.1093/bioinformatics/btx699

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels, Philip et al. “MultiQC: summarize analysis results for multiple tools and samples in a single report.” Bioinformatics (Oxford, England) vol. 32,19 (2016): 3047-8. doi:10.1093/bioinformatics/btw354

- [picard-tools](http://broadinstitute.github.io/picard)

- [prokka](https://pubmed.ncbi.nlm.nih.gov/24642063/)

  > Seemann, Torsten. “Prokka: rapid prokaryotic genome annotation.” Bioinformatics (Oxford, England) vol. 30,14 (2014): 2068-9. doi:10.1093/bioinformatics/btu153

- [QUAST](https://www.ncbi.nlm.nih.gov/pubmed/23422339/)

  > Gurevich, Alexey et al. “QUAST: quality assessment tool for genome assemblies.” Bioinformatics (Oxford, England) vol. 29,8 (2013): 1072-5. doi:10.1093/bioinformatics/btt086

- [SAMtools](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198575/)

  > Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. Epub 2011 Sep 8. PMID: 21903627; PMCID: PMC3198575.

- [SPAdes](https://www.ncbi.nlm.nih.gov/pubmed/24093227/)

  > Bankevich, Anton et al. “SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.” Journal of computational biology : a journal of computational molecular cell biology vol. 19,5 (2012): 455-77. doi:10.1089/cmb.2012.0021

- [SSPACE Basic](https://pubmed.ncbi.nlm.nih.gov/21149342/)

  > Boetzer, Marten et al. “Scaffolding pre-assembled contigs using SSPACE.” Bioinformatics (Oxford, England) vol. 27,4 (2011): 578-9. doi:10.1093/bioinformatics/btq683

- [Trimmomatic](https://pubmed.ncbi.nlm.nih.gov/24695404/)

  > Bolger, Anthony M et al. “Trimmomatic: a flexible trimmer for Illumina sequence data.” Bioinformatics (Oxford, England) vol. 30,15 (2014): 2114-20. doi:10.1093/bioinformatics/btu170

- [Trinity](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712/)

  > Haas, Brian J et al. “De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.” Nature protocols vol. 8,8 (2013): 1494-512. doi:10.1038/nprot.2013.084

- [UMI-tools](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340976/)

  > Smith, Tom et al. “UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.” Genome research vol. 27,3 (2017): 491-499. doi:10.1101/gr.209601.116

- [vRhyme](https://pubmed.ncbi.nlm.nih.gov/35544285/)

  > Kieft, Kristopher et al. “vRhyme enables binning of viral genomes from metagenomes.” Nucleic acids research vol. 50,14 (2022): e83. doi:10.1093/nar/gkac341

- [VSEARCH](https://pubmed.ncbi.nlm.nih.gov/27521926/)

  > Rognes, Torbjørn et al. “VSEARCH: a versatile open source tool for metagenomics.” PeerJ vol. 4 e2584. 18 Oct. 2016, doi:10.7717/peerj.2584

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/bbmap/bbduk/meta.yml cpan
modules/nf-core/bcftools/consensus/meta.yml cpan
modules/nf-core/bcftools/filter/meta.yml cpan
modules/nf-core/bcftools/mpileup/meta.yml cpan
modules/nf-core/bcftools/norm/meta.yml cpan
modules/nf-core/bcftools/sort/meta.yml cpan
modules/nf-core/bcftools/stats/meta.yml cpan
modules/nf-core/bedtools/maskfasta/meta.yml cpan
modules/nf-core/bedtools/merge/meta.yml cpan
modules/nf-core/blast/makeblastdb/meta.yml cpan
modules/nf-core/bowtie2/align/meta.yml cpan
modules/nf-core/bowtie2/build/meta.yml cpan
modules/nf-core/bracken/bracken/meta.yml cpan
modules/nf-core/bwamem2/index/meta.yml cpan
modules/nf-core/bwamem2/mem/meta.yml cpan
modules/nf-core/cat/cat/meta.yml cpan
modules/nf-core/cdhit/cdhitest/meta.yml cpan
modules/nf-core/checkv/downloaddatabase/meta.yml cpan
modules/nf-core/checkv/endtoend/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/emboss/cons/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/ivar/consensus/meta.yml cpan
modules/nf-core/ivar/variants/meta.yml cpan
modules/nf-core/kaiju/kaiju/meta.yml cpan
modules/nf-core/kaiju/kaiju2table/meta.yml cpan
modules/nf-core/kraken2/kraken2/meta.yml cpan
modules/nf-core/mafft/meta.yml cpan
modules/nf-core/megahit/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/muscle/meta.yml cpan
modules/nf-core/picard/collectmultiplemetrics/meta.yml cpan
modules/nf-core/picard/markduplicates/meta.yml cpan
modules/nf-core/quast/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/flagstat/meta.yml cpan
modules/nf-core/samtools/idxstats/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/stats/meta.yml cpan
modules/nf-core/seqkit/grep/meta.yml cpan
modules/nf-core/spades/meta.yml cpan
modules/nf-core/tabix/tabix/meta.yml cpan
modules/nf-core/trimmomatic/meta.yml cpan
modules/nf-core/trinity/meta.yml cpan
modules/nf-core/umitools/dedup/meta.yml cpan
modules/nf-core/umitools/extract/meta.yml cpan
modules/nf-core/untar/meta.yml cpan
modules/nf-core/vsearch/cluster/meta.yml cpan
subworkflows/nf-core/bam_stats_samtools/meta.yml cpan
subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml cpan
pyproject.toml pypi