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assemblebac-ont

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

https://github.com/avantonder/assemblebac-ont

Science Score: 67.0%

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Keywords

assembly bacteria bacterial-genome-analysis bacterial-genomes nextflow nextflow-pipeline ont
Last synced: 6 months ago · JSON representation ·

Repository

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

Basic Info
  • Host: GitHub
  • Owner: avantonder
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 3.18 MB
Statistics
  • Stars: 8
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 7
Topics
assembly bacteria bacterial-genome-analysis bacterial-genomes nextflow nextflow-pipeline ont
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

assembleBAC-ONT

avantonder/assembleBAC-ONT

Cite with Zenodo

Nextflow run with conda run with docker run with singularity

Introduction

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

  1. Read QC (FastQC or falco as an alternative option)
  2. Performs optional read pre-processing
  3. Downsample fastq files (Rasusa)
  4. de novo assembly (Flye)
  5. Polish assemblies with ONT data (Medaka)
  6. Assembly metrics (Quast)
  7. Assembly completeness (CheckM2)
  8. Sequence Type assignment (mlst)
  9. Annotation (Bakta)
  10. Present QC, visualisation and custom reporting for filtering and assembly 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.

You will need to Download the Bakta light database (Bakta version 1.10.4 is required to run the amrfinder_update command):

bash wget https://zenodo.org/record/7669534/files/db-light.tar.gz tar -xzf db-light.tar.gz rm db-light.tar.gz amrfinder_update --force_update --database db-light/amrfinderplus-db/

Additionally, you will need to download the CheckM2 database (CheckM2 is required):

bash checkm2 database --download --path path/to/checkm2db

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file with 2 columns, and a header row as shown in the example below. An executable Python script called build_samplesheet.py has been provided to auto-create an input samplesheet based on a directory containing sub-directories with the prefix barcode which contain the FastQ files before you run the pipeline (requires Python 3 installed locally) e.g.

```bash wget -L https://github.com/avantonder/assembleBAC-ONT/blob/master/assets/build_samplesheet.py

python buildsamplesheet.py -i <FASTQDIR> ```

csv title="samplesheet.csv" sample,fastq SAMPLE_1,path/to/fastq/file1 SAMPLE_1,path/to/fastq/file2 SAMPLE_2,path/to/fastq/file1

Now you can run the pipeline using:

bash nextflow run avantonder/assembleBAC-ONT \ -profile singularity \ -c <INSTITUTION>.config \ --input samplesheet.csv \ --genome_size <ESTIMATED GENOME SIZE e.g. 4M> \ --medaka_model <MEDAKA MODEL> \ --outdir <OUTDIR> \ --baktadb path/to/baktadb/dir \ --checkm2db path/to/checkm2db/dir/uniref100.KO.1.dmnd \ -resume

See usage docs for all of the available options when running the pipeline.

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (<INSTITUTION>.config in the example command above). You can chain multiple config profiles in a comma-separated string.

  • The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
  • Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
  • If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
  • If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

Documentation

The avantonder/assembleBAC-ONT pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

avantonder/assembleBAC-ONT was originally written by Andries van Tonder. I wouldn't have been able to write this pipeline with out the tools, documentation, pipelines and modules made available by the fantastic nf-core community. In particular, the excellent viralrecon pipeline was a source of code and inspiration. Finally, a shout out to Robert Petit's Dragonflye as an additional source of inspiration.

Feedback

If you have any issues, questions or suggestions for improving assembleBAC-ONT, please submit them to the Issue Tracker.

Citations

If you use the avantonder/assembleBAC-ONT pipeline, please cite it using the following doi: 10.5281/zenodo.15040673

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

Owner

  • Login: avantonder
  • Kind: user

Citation (CITATIONS.md) 

# avantonder/assembleBAC-ONT: 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

- [Bakta](https://pubmed.ncbi.nlm.nih.gov/34739369/)
  
  > Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. doi: 10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.

- [CheckM2](https://pubmed.ncbi.nlm.nih.gov/37500759/)
  >Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023 Aug;20(8):1203-1212. doi: 10.1038/s41592-023-01940-w. Epub 2023 Jul 27. Erratum in: Nat Methods. 2024 Apr;21(4):735. doi: 10.1038/s41592-024-02248-z. PMID: 37500759.

- [Falco](https://falco.readthedocs.io/)

  > de Sena Brandine G, Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Res. 2019 Nov 7;8:1874. doi: 10.12688/f1000research.21142.2. PMID: 33552473; PMCID: PMC7845152.

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

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

- [Filtlong](https://github.com/rrwick/Filtlong)

- [Flye](https://pubmed.ncbi.nlm.nih.gov/30936562/)
  
  > Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. doi: 10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.

- [Medaka](https://github.com/nanoporetech/medaka)

- [Mash](https://pubmed.ncbi.nlm.nih.gov/27323842/)
    
    > Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. PMID: 27323842; PMCID: PMC4915045.

- [mlst](https://github.com/tseemann/mlst)

- [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.

- [nanoq](https://github.com/esteinig/nanoq)

  > Steinig, E, Coin, L. 2022. Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69). 

- [Porechop](https://github.com/rrwick/Porechop)

  > Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 2017 Sep 14;3(10):e000132. doi: 10.1099/mgen.0.000132. PMID: 29177090; PMCID: PMC5695209.

- [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI)

  > Bonenfant Q, Noé L, Touzet H. Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinform Adv. 2022 Nov 21;3(1):vbac085. doi: 10.1093/bioadv/vbac085. PMID: 36698762; PMCID: PMC9869717.

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

  > Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PubMed PMID: 23422339; PubMed Central PMCID: PMC3624806.

- [Rasusa](https://github.com/mbhall88/rasusa)
  
  > Hall MB. Rasusa: Randomly subsample sequencing reads to a specified coverage. 2019. doi:10.5281/zenodo.3731394

## 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

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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/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi