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denovotranscript

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

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

Science Score: 57.0%

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    Found 10 DOI reference(s) in README
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Keywords

denovo-assembly nextflow nf-core pipeline rna-seq transcriptome workflow
Last synced: 6 months ago · JSON representation ·

Repository

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

Basic Info
Statistics
  • Stars: 16
  • Watchers: 185
  • Forks: 4
  • Open Issues: 5
  • Releases: 3
Topics
denovo-assembly nextflow nf-core pipeline rna-seq transcriptome workflow
Created over 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/denovotranscript

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

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

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Introduction

nf-core/denovotranscript is a bioinformatics pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. It takes a samplesheet and FASTQ files as input, perfoms quality control (QC), trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It outputs a transcriptome assembly FASTA file, a transcript abundance TSV file, and a MultiQC report with assembly quality and read QC metrics.

nf-core/transfuse metro map

  1. Read QC of raw reads (FastQC)
  2. Adapter and quality trimming (fastp)
  3. Read QC of trimmed reads (FastQC)
  4. Remove rRNA or mitochondrial DNA (optional) (SortMeRNA)
  5. Transcriptome assembly using any combination of the following:
  • Trinity with normalised reads (default=True)
  • Trinity with non-normalised reads
  • rnaSPAdes medium filtered transcripts outputted (default=True)
  • rnaSPAdes soft filtered transcripts outputted
  • rnaSPAdes hard filtered transcripts outputted
  1. Redundancy reduction with Evidential Gene tr2aacds. A transcript to gene mapping is produced from Evidential Gene's outputs using gawk.
  2. Assembly completeness QC (BUSCO)
  3. Other assembly quality metrics (rnaQUAST)
  4. Transcriptome quality assessment with TransRate, including the use of reads for assembly evaluation. This step is not performed if profile is set to conda or mamba.
  5. Pseudo-alignment and quantification (Salmon)
  6. HTML report for raw reads, trimmed reads, BUSCO, and Salmon (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 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a pair of fastq files (paired end).

Now, you can run the pipeline using:

bash nextflow run nf-core/denovotranscript \ -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.

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

Pipeline output

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/denovotranscript was written by Avani Bhojwani (@avani-bhojwani) and Timothy Little (@timslittle).

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 #denovotranscript channel (you can join with this invite).

Citations

If you use nf-core/denovotranscript for your analysis, please cite it using the following doi: 10.5281/zenodo.13324371

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: 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/denovotranscript: 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

- [BUSCO](https://busco.ezlab.org/)

  > Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021 Sep 27;38(10):4647-4654. doi: 10.1093/molbev/msab199. PMID: 34320186; PMCID: PMC8476166.

- [Evidential Gene](http://arthropods.eugenes.org/EvidentialGene/)

  > Gilbert, D. G. (2019). Longest protein, longest transcript or most expression, for accurate gene reconstruction of transcriptomes? bioRxiv. https://doi.org/10.1101/829184

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

  > Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta. 2023 May 8;2(2):e107. doi: 10.1002/imt2.107. PMID: 38868435; PMCID: PMC10989850.

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

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

- [gawk](https://www.gnu.org/software/gawk/)

- [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.

- [rnaQUAST](https://github.com/ablab/rnaquast)

  > Bushmanova E, Antipov D, Lapidus A, Suvorov V, Prjibelski AD. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics. 2016 Jul 15;32(14):2210-2. doi: 10.1093/bioinformatics/btw218. Epub 2016 Apr 23. PMID: 27153654.

- [rnaSPAdes](https://ablab.github.io/spades/rna.html)

  > Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102. PMID: 32559359.

- [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html)

  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PMID: 28263959; PMCID: PMC5600148.

- [SortMeRNA](https://github.com/sortmerna/sortmerna)

  > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PMID: 23071270.

- [TransRate](https://hibberdlab.com/transrate/)

  > Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S. TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Res. 2016 Aug;26(8):1134-44. doi: 10.1101/gr.196469.115. Epub 2016 Jun 1. PMID: 27252236; PMCID: PMC4971766.

  This pipeline uses TransRate from the [Oyster River Protocol](https://github.com/macmanes-lab/Oyster_River_Protocol/tree/master/software).

  > MacManes MD. The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. PeerJ. 2018 Aug 3;6:e5428. doi: 10.7717/peerj.5428. PMID: 30083482; PMCID: PMC6078068.

- [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki)

  > Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PMID: 23845962; PMCID: PMC3875132.

## 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
  • Create event: 14
  • Release event: 2
  • Issues event: 15
  • Watch event: 14
  • Delete event: 11
  • Member event: 1
  • Issue comment event: 19
  • Push event: 64
  • Pull request review event: 35
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  • Pull request event: 49
  • Fork event: 2
Last Year
  • Create event: 14
  • Release event: 2
  • Issues event: 15
  • Watch event: 14
  • Delete event: 11
  • Member event: 1
  • Issue comment event: 19
  • Push event: 64
  • Pull request review event: 35
  • Pull request review comment event: 20
  • Pull request event: 49
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 14
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 7
  • Total pull request authors: 4
  • Average comments per issue: 0.88
  • Average comments per pull request: 0.5
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 14
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Issue authors: 7
  • Pull request authors: 4
  • Average comments per issue: 0.88
  • Average comments per pull request: 0.5
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • IdoBar (3)
  • shellywanamaker (1)
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  • devjanee (1)
  • avani-bhojwani (1)
  • dppss90008 (1)
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Pull Request Authors
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  • nf-core-bot (7)
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Top Labels
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bug (7) enhancement (2)
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Dependencies

modules/nf-core/busco/busco/meta.yml cpan
modules/nf-core/cat/cat/meta.yml cpan
modules/nf-core/cat/fastq/meta.yml cpan
modules/nf-core/evigene/tr2aacds/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/gawk/meta.yml cpan
modules/nf-core/salmon/index/meta.yml cpan
modules/nf-core/salmon/quant/meta.yml cpan
modules/nf-core/sortmerna/meta.yml cpan
modules/nf-core/spades/meta.yml cpan
modules/nf-core/trinity/meta.yml cpan
subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml cpan
modules/local/orp_transrate/Dockerfile docker
  • ubuntu 20.04 build
.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v4 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
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modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/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/fastqc/environment.yml conda
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modules/nf-core/multiqc/environment.yml conda
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modules/nf-core/busco/busco/environment.yml pypi
modules/nf-core/cat/cat/environment.yml pypi
modules/nf-core/cat/fastq/environment.yml pypi
modules/nf-core/evigene/tr2aacds/environment.yml pypi
modules/nf-core/fastp/environment.yml pypi
modules/nf-core/gawk/environment.yml pypi
modules/nf-core/salmon/index/environment.yml pypi
modules/nf-core/salmon/quant/environment.yml pypi
modules/nf-core/sortmerna/environment.yml pypi
modules/nf-core/spades/environment.yml pypi
modules/nf-core/trinity/environment.yml pypi