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samurai

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

https://github.com/dincalcilab/samurai

Science Score: 67.0%

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Keywords

bioinformatics bioinformatics-pipeline nextflow nextflow-pipeline
Last synced: 6 months ago · JSON representation ·

Repository

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

Basic Info
  • Host: GitHub
  • Owner: DIncalciLab
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 4.01 MB
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 0
  • Open Issues: 16
  • Releases: 14
Topics
bioinformatics bioinformatics-pipeline nextflow nextflow-pipeline
Created almost 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

SAMURAI: Shallow Analysis of Copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline

戦の勝負は、将と士卒の気によるのみなり。

(The outcome of the battle depends on the spirit of the commander and the men.)

Minamoto no Yoshitsune (1159-1189)

Introduction

SAMURAI is a bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs). It supports a number of workflows depending on the nature of the samples (coming from tissues or other biological fluids like plasma). While it was developed with cancer studies in mind, it is applicable to any field where DNA alterations need to be studied.

The pipeline is built using Nextflow, 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 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 in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

A preprint describing SAMURAI and its applications to artificial and real-world data sets is available on BiorXiv.

Pipeline summary

  1. Read QC (FastQC)
  2. (Optional) Trim reaads based on quality scores and extract unique molecular identifiers (UMIs) if applicable (fastp)
  3. Align reads to the reference genome (BWA)
  4. Run quality control checks on the aligned reads (Picard)
  5. Perform copy number alteration identification for tissue samples(QDNAseq, ASCAT.sc)
  6. (Optional) Perform size selection on samples from liquid biopsies(sambamba)
  7. Perform copy number alteration identification for liquid biopsy samples(ichorCNA, WisecondorX)
  8. (Optional) Extract copy number instability signatures (CINSignatureQuantification)
  9. (Optional) Identify recurrent altered regions in the sample population (GISTIC)
  10. (Optional) Compute HRDCNA Score to detect Homologous recombination deficiency (HRD) (HRDCNA)
  11. Present QC for each sep of the pipeline (MultiQC)

Quick Start

  1. Install Nextflow (>=23.10.1)

  2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

  3. Download the pipeline and test it on a minimal dataset with a single command.

We included a test for the solid_biopsy subworkflow that demonstrates its functionality with ASCAT.sc. You can run it with the following command:

bash nextflow run dincalcilab/samurai -profile test,YOURPROFILE --outdir <OUTDIR>

We included also a test for the liquid_biopsy subworkflow that demonstrates its functionality with ichorCNA. You can run it with the following command:

bash nextflow run dincalcilab/samurai -profile test_ichorcna,YOURPROFILE --outdir <OUTDIR>

Note: A working internet connection which allows connection to the AWS S3 service is required to run the tests

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 (YOURPROFILE 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.
  1. Start running your own analysis!

bash nextflow run dincalcilab/samurai --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> <pipeline options>

Credits

dincalcilab/samurai was originally written by Sara Potente and Luca Beltrame.

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

  • Laura Mannarino
  • Riccardo Zadro

Contributions and Support

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

Citations

If you use dincalcilab/samurai for your analysis, please cite SAMURAI article as follows:

Sara Potente, Diego Boscarino, Dino Paladin, Sergio Marchini, Luca Beltrame, Chiara Romualdi, SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline, Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbaf035, https://doi.org/10.1093/bib/bbaf035

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: DIncalciLab
  • Login: DIncalciLab
  • Kind: organization
  • Location: Italy

Citation (CITATIONS.md) 

# dincalcilab/samurai: 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

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

- [Fastp](https://pubmed.ncbi.nlm.nih.gov/30423086/)

  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281.

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

  > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PMID: 19451168; PMCID: PMC2705234.

- [Samtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943; PMCID: PMC2723002.

- [Sambamba](https://pubmed.ncbi.nlm.nih.gov/25697820/)

  > Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics. 2015 Jun 15;31(12):2032-4. doi: 10.1093/bioinformatics/btv098. Epub 2015 Feb 19. PMID: 25697820; PMCID: PMC4765878.

- [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.

- [QDNAseq](https://pubmed.ncbi.nlm.nih.gov/25236618/)

  > Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 2014 Dec;24(12):2022-32. doi: 10.1101/gr.175141.114. Epub 2014 Sep 18. PMID: 25236618; PMCID: PMC4248318.

- [ichorCNA](https://pubmed.ncbi.nlm.nih.gov/29109393/)

  > Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O'Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017 Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y. PMID: 29109393; PMCID: PMC5673918.

- [ASCAT.sc](https://github.com/VanLoo-lab/ASCAT.sc)

- [CINSignatureQuantification](https://pubmed.ncbi.nlm.nih.gov/35705807/)

  > Drews RM, Hernando B, Tarabichi M, Haase K, Lesluyes T, Smith PS, Morrill Gavarró L, Couturier DL, Liu L, Schneider M, Brenton JD, Van Loo P, Macintyre G, Markowetz F. A pan-cancer compendium of chromosomal instability. Nature. 2022 Jun;606(7916):976-983. doi: 10.1038/s41586-022-04789-9. Epub 2022 Jun 15. PMID: 35705807; PMCID: PMC7613102.

- [HRDCNA](https://www.nature.com/articles/s42003-023-04901-3)

  > Yao, H., Li, H., Wang, J. et al. Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology. Commun Biol 6, 527 (2023). https://doi.org/10.1038/s42003-023-04901-3

- [WisecondorX](https://pubmed.ncbi.nlm.nih.gov/30566647/)

  > Raman L, Dheedene A, De Smet M, Van Dorpe J, Menten B. WisecondorX: improved copy number detection for routine shallow whole-genome sequencing. Nucleic Acids Res. 2019 Feb 28;47(4):1605-1614. doi: 10.1093/nar/gky1263. PMID: 30566647; PMCID: PMC6393301.

- [WisecondorX - Copy number profile abnormality (CPA)](https://pubmed.ncbi.nlm.nih.gov/32317009/)

  > Raman L, Van der Linden M, Van der Eecken K, Vermaelen K, Demedts I, Surmont V, Himpe U, Dedeurwaerdere F, Ferdinande L, Lievens Y, Claes K, Menten B, Van Dorpe J. Shallow whole-genome sequencing of plasma cell-free DNA accurately differentiates small from non-small cell lung carcinoma. Genome Med. 2020 Apr 21;12(1):35. doi: 10.1186/s13073-020-00735-4. PMID: 32317009; PMCID: PMC7175544.

- [GISTIC](https://pubmed.ncbi.nlm.nih.gov/21527027/)

  > Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12(4):R41. doi: 10.1186/gb-2011-12-4-r41. Epub 2011 Apr 28. PMID: 21527027; PMCID: PMC3218867.

- [maftools](https://pubmed.ncbi.nlm.nih.gov/30341162/)

  > Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018 Nov;28(11):1747-1756. doi: 10.1101/gr.239244.118. Epub 2018 Oct 19. PMID: 30341162; PMCID: PMC6211645.

- [deepTools](https://pubmed.ncbi.nlm.nih.gov/24799436/)
  > Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91. doi: 10.1093/nar/gku365. Epub 2014 May 5. PMID: 24799436; PMCID: PMC4086134.

## 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)

- [Podman](https://zenodo.org/records/4735634)

- [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/ci.yml actions
  • actions/checkout v4 composite
  • jlumbroso/free-disk-space v1.3.1 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
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.github/workflows/linting.yml actions
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  • actions/upload-artifact 5d5d22a31266ced268874388b861e4b58bb5c2f3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/linting_comment.yml actions
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  • marocchino/sticky-pull-request-comment 331f8f5b4215f0445d3c07b4967662a32a2d3e31 composite
modules/nf-core/bowtie2/align/meta.yml cpan
modules/nf-core/bowtie2/build/meta.yml cpan
modules/nf-core/bwa/index/meta.yml cpan
modules/nf-core/bwa/mem/meta.yml cpan
modules/nf-core/bwamem2/index/meta.yml cpan
modules/nf-core/bwamem2/mem/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/dragmap/align/meta.yml cpan
modules/nf-core/dragmap/hashtable/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/hmmcopy/readcounter/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/picard/collecthsmetrics/meta.yml cpan
modules/nf-core/picard/collectmultiplemetrics/meta.yml cpan
modules/nf-core/picard/collectwgsmetrics/meta.yml cpan
modules/nf-core/picard/markduplicates/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/samtools/view/meta.yml cpan
modules/nf-core/snapaligner/align/meta.yml cpan
modules/nf-core/snapaligner/index/meta.yml cpan
modules/nf-core/wisecondorx/convert/meta.yml cpan
modules/nf-core/wisecondorx/newref/meta.yml cpan
modules/nf-core/wisecondorx/predict/meta.yml cpan
subworkflows/nf-core/bam_markduplicates_picard/meta.yml cpan
subworkflows/nf-core/bam_qc_picard/meta.yml cpan
subworkflows/nf-core/bam_sort_stats_samtools/meta.yml cpan
subworkflows/nf-core/bam_stats_samtools/meta.yml cpan
subworkflows/nf-core/fasta_index_dna/meta.yml cpan
subworkflows/nf-core/fastq_align_bwa/meta.yml cpan
subworkflows/nf-core/fastq_align_dna/meta.yml cpan
subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
modules/nf-core/bowtie2/align/environment.yml pypi
modules/nf-core/bowtie2/build/environment.yml pypi
modules/nf-core/bwa/index/environment.yml pypi
modules/nf-core/bwa/mem/environment.yml pypi
modules/nf-core/bwamem2/index/environment.yml pypi
modules/nf-core/bwamem2/mem/environment.yml pypi
modules/nf-core/custom/dumpsoftwareversions/environment.yml pypi
modules/nf-core/dragmap/align/environment.yml pypi
modules/nf-core/dragmap/hashtable/environment.yml pypi
modules/nf-core/fastp/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/hmmcopy/readcounter/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/picard/collecthsmetrics/environment.yml pypi
modules/nf-core/picard/collectmultiplemetrics/environment.yml pypi
modules/nf-core/picard/collectwgsmetrics/environment.yml pypi
modules/nf-core/picard/markduplicates/environment.yml pypi
modules/nf-core/samtools/faidx/environment.yml pypi
modules/nf-core/samtools/flagstat/environment.yml pypi
modules/nf-core/samtools/idxstats/environment.yml pypi
modules/nf-core/samtools/index/environment.yml pypi
modules/nf-core/samtools/sort/environment.yml pypi
modules/nf-core/samtools/stats/environment.yml pypi
modules/nf-core/samtools/view/environment.yml pypi
modules/nf-core/snapaligner/align/environment.yml pypi
modules/nf-core/snapaligner/index/environment.yml pypi
modules/nf-core/wisecondorx/convert/environment.yml pypi
modules/nf-core/wisecondorx/newref/environment.yml pypi
modules/nf-core/wisecondorx/predict/environment.yml pypi
pyproject.toml pypi