Data

Tools

Indexes

Applications

Experiments

Open Source Science

oceanomics-oceangenomes-ref-genomes

OceanOmics-OceanGenomes reference genomes pipeline

https://github.com/computational-biology-oceanomics/oceanomics-oceangenomes-ref-genomes

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 7 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization computational-biology-oceanomics has institutional domain (www.uwa.edu.au)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

OceanOmics-OceanGenomes reference genomes pipeline

Basic Info
  • Host: GitHub
  • Owner: Computational-Biology-OceanOmics
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Size: 8.12 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 2
  • Open Issues: 0
  • Releases: 2
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

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

Introduction

This pipeline is designed for the de novo genome assembly and analysis of high-quality marine vertebrate genomes as part of the Minderoo OceanOmics Ocean Genomes Project. It processes raw HiFi and Hi-C data, performs assembly, scaffolding, decontamination, generates key assembly statistics and prepares the genome for manual curation within pretext map.

OceanOmics Reference Genome Pipeline Overview

  1. Filter and convert bam files to fastq files (HiFiAdapterFilt)
  2. PacBio Read QC (FastQC)
  3. Count k-mers (Meryl)
  4. Estimate genome size (GenomeScope2)
  5. Assemble hifi data (Hifiasm)
  6. Assembly stats on hifi data (Gfastats)
  7. Illumina Read QC (FastQC)
  8. Assemble Pacbio & Illumina reads (Hifiasm)
  9. Assembly stats (Gfastats)
  10. Gene assembly QC (BUSCO)
  11. K-mer assembly QC (Merqury)
  12. Create index (Samtools)
  13. Index assemble and align Hi-C reads (BWA)
  14. Map pairs (Pairtools)
  15. Sort and index (Samtools)
  16. Create scaffold (YAHS)
  17. Create decontamination report (fcs-gx)
  18. Create decontamination report (Tiara)
  19. Filter decontaminated scaffolds (BBMap)
  20. Scaffold stats (Gfastats)
  21. Scaffold QC (BUSCO)
  22. Scaffold QC (Merqury)
  23. Generate coverage tracks (minimap2)
  24. Generate coverage tracks (`bedtools)
  25. Predict telomere locations (tidk)
  26. Align reads to scaffolds (BWA)
  27. Align reads to scaffolds (Pairtools)
  28. Generate pretext maps (PretextMap)
  29. Inject coverage tracks into pretext map (PretextGraph)
  30. Present QC for raw reads (MultiQC)

Usage

[!NOTE] If you are new to Nextflow, please refer to this page on how to set-up Nextflow.

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

samplesheet.csv:

csv sample,hifi_dir,hic_dir,version,date,tolid,taxid,species OG88,hifi_bams/OG89,hic_fastqs/OG89,hic1,v240101,OG88,163129,Ophthalmolepis lineolata OG89,hifi_bams/OG89,,hifi1,v240202,OG88,163129,Ophthalmolepis lineolata OG90,hifi_fastqs/OG90,hic_fastqs/OG90,hic1,v240303,OG88,163129,Ophthalmolepis lineolata

Each row represents a sample. The hifidir column must point to a directory that contains bam files or fastq files. The hicdir column can point to a directory containing fastq files, however this column can be left blank if there isn't Hi-C data for this sample. Taxid refers to the NCBI taxon ID for that samples.

Now, you can run the pipeline using:

bash nextflow run Computational-Biology-OceanOmics/OceanGenomes-refgenomes \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> \ --buscodb /path/to/buscodb \ --gxdb /path/to/gxdb \ --binddir /scratch \ --scaffolder <yahs or salsa> --tempdir <tempdir> -c pawsey_profile.config \ -resume \ -with-report

This repository contains a custom config file to run the pipeline on the pawsey supercomputer with slurm.

[!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. For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

For details about the output files and reports, please refer to the output documentation.

Credits

Computational-Biology-OceanOmics/OceanOmics-OceanGenomes-ref-genomes was originally adapted from the Vertebrate Genome project Galaxy pipeline (https://galaxyproject.org/projects/vgp/) by Emma de Jong and was converted to Nextflow by Adam Bennett and Lauren Huet. This version was built on top of the nf-core template.

Citations

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

Owner

  • Name: Computational-Biology-OceanOmics
  • Login: Computational-Biology-OceanOmics
  • Kind: organization

This is the research and development space for the OceanOmics team

Citation (CITATIONS.md) 

# Computational-Biology-OceanOmics/OceanGenomes-refgenomes: Citations

## [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

- [HiFiAdapterFilt](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08375-1)

  > Sim, S.B., Corpuz, R.L., Simmonds, T.J. et al. HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly. BMC Genomics 23, 157 (2022). doi: 10.1186/s12864-022-08375-1

- [Meryl](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02134-9)

  > Rhie, A., Walenz, B.P., Koren, S. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). doi: 10.1186/s13059-020-02134-9

- [GenomeScope2](https://www.nature.com/articles/s41467-020-14998-3)

  > Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 11, 1432 (2020). doi: 10.1038/s41467-020-14998-3

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

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

- [Hifiasm](https://www.nature.com/articles/s41592-020-01056-5)

  > Cheng, H., Concepcion, G.T., Feng, X. et al. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021). doi: 10.1038/s41592-020-01056-5

- [BWA](https://pubmed.ncbi.nlm.nih.gov/19451168/)

  > Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–1760. doi: 10.1093/bioinformatics/btp324

- [Pairtools](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9949071/)

  > Open2C, Abdennur, N., Fudenberg, G., Flyamer, I. M., Galitsyna, A. A., Goloborodko, A., Imakaev, M., & Venev, S. V. (2023). Pairtools: from sequencing data to chromosome contacts. bioRxiv : the preprint server for biology, 2023.02.13.528389. doi: 10.1101/2023.02.13.528389

- [Samtools](https://academic.oup.com/bioinformatics/article/25/16/2078/204688)

  > Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, August 2009, Pages 2078–2079, doi: 10.1093/bioinformatics/btp352

- [YAHS](https://academic.oup.com/bioinformatics/article/39/1/btac808/6917071)

  > Chenxi Zhou, Shane A McCarthy, Richard Durbin, YaHS: yet another Hi-C scaffolding tool, Bioinformatics, Volume 39, Issue 1, January 2023, btac808, doi: 10.1093/bioinformatics/btac808

- [fcs-gx](https://www.biorxiv.org/content/10.1101/2023.06.02.543519v1)

  > Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. Rapid and sensitive detection of genome contamination at scale with FCS-GX. biorXiv. (2023).

- [Tiara](https://academic.oup.com/bioinformatics/article/38/2/344/6375939)

  > Michał Karlicki, Stanisław Antonowicz, Anna Karnkowska, Tiara: deep learning-based classification system for eukaryotic sequences, Bioinformatics, Volume 38, Issue 2, 15 January 2022, Pages 344–350, doi: 10.1093/bioinformatics/btab672

- [BBMap](https://escholarship.org/uc/item/1h3515gn)

  > Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner. Lawrence Berkeley National Laboratory. LBNL Report #: LBNL-7065E.

- [Gfastats](https://academic.oup.com/bioinformatics/article/38/17/4214/6633308)

  > Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, doi: 10.1093/bioinformatics/btac460

- [BUSCO](https://academic.oup.com/mbe/article/38/10/4647/6329644)

  > Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov, BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654

- [Merqury](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02134-9)

  > Rhie, A., Walenz, B.P., Koren, S. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020). doi: 10.1186/s13059-020-02134-9

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

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## 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.

GitHub Events

Total
  • Release event: 1
  • Push event: 14
  • Public event: 1
  • Pull request event: 4
  • Fork event: 2
  • Create event: 2
Last Year
  • Release event: 1
  • Push event: 14
  • Public event: 1
  • Pull request event: 4
  • Fork event: 2
  • Create event: 2