pacvar
Longread PacBio sequencing processing for WGS and PureTarget
Science Score: 57.0%
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Low similarity (9.6%) to scientific vocabulary
Keywords
Repository
Longread PacBio sequencing processing for WGS and PureTarget
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: master
- Homepage: https://nf-co.re/pacvar
- Size: 345 MB
Statistics
- Stars: 10
- Watchers: 197
- Forks: 6
- Open Issues: 8
- Releases: 2
Topics
Metadata Files
README.md
Introduction
nf-core/pacvar is a bioinformatics pipeline that processes long-read PacBio data. Specifically, the pipeline provides two workflows: one for processing whole-genome sequencing data, and another for processing reads from the PureTarget expansion panel offered by PacBio. This second workflow characterizes tandem repeats. Because the pipeline is designed for PacBio reads, it uses PacBio’s officially released tools.
Workflow Overview
WGS Workflow Overview
- Choice of SNP calling routes:
a. (
deepvariant) b. (HaplotypeCaller) - Call SVs (
pbsv) - Index VCF files (
bcftools) - Phase SNPs, SVs and BAM files (
hiphase)
Tandem Repeat Workflow Overview
- Genotype tandem repeats - produce spanning bams and vcf (
TRGT) - Index and Sort tandem tepeat spanning bam (
SAMtools) - Plot repeat motif plots (
TRGT) - Sort spanning VCF (
bcftools)
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 testbefore running the workflow on actual data.
First, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
csv
sample,bam,pbi
CONTROL,AEG588A1_S1_L002_R1_001.bam,AEG588A1_S1_L002_R1_001.pbi
Note that the .pbi file is not required. If you choose not to include it, your input file might look like this:
csv
sample,bam,pbi
CONTROL,AEG588A1_S1_L002_R1_001.bam
Each row represents an unaligned bam file and their associated index (optional).
Now, you can run the pipeline. Below is an example
bash
nextflow run nf-core/pacvar \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--workflow <wgs/repeat> \
--barcodes barcodes.bed \
--intervals intervals.bed \
--genome <GENOME NAME (e.g. GATK.GRCh38)> \
--outdir <OUTDIR>
optional paramaters include: --skip_demultiplexing, --skip_snp, --skip_sv, --skip_phase.
[!WARNING] Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs. Please provide pipeline parameters via the CLI or Nextflow-params-fileoption. Custom config files including those provided by the-cNextflow 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/pacvar was originally written by Tanya Sarkin Jain.
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 #pacvar channel (you can join with this invite).
Citations
If you use nf-core/pacvar for your analysis, please cite it using the following doi: 10.5281/zenodo.14813048
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
- Website: http://nf-co.re
- Twitter: nf_core
- Repositories: 84
- Profile: https://github.com/nf-core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Citation (CITATIONS.md)
# nf-core/pacvar: 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/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [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. - [lima](https://github.com/PacificBiosciences/barcoding) - [pbmm2](https://github.com/PacificBiosciences/pbmm2) - [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. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. - [deepvariant](https://pubmed.ncbi.nlm.nih.gov/30247488/) > Poplin, R., Chang, PC., Alexander, D. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36, 983–987 (2018). https://doi.org/10.1038/nbt.4235 - [HaplotypeCaller](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thibault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples bioRxiv, 201178. DOI: 10.1101/201178 - [bcftools](https://pubmed.ncbi.nlm.nih.gov/33590861/) > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819. - [HiPhase](https://pubmed.ncbi.nlm.nih.gov/38269623/) > Holt JM, Saunders CT, Rowell WJ, Kronenberg Z, Wenger AM, Eberle M. HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics. 2024 Feb 1;40(2):btae042. doi: 10.1093/bioinformatics/btae042. PMID: 38269623; PMCID: PMC10868326. - [pbsv](https://github.com/PacificBiosciences/pbsv) - [TRGT](https://github.com/PacificBiosciences/trgt) ## 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: 12
- Release event: 1
- Issues event: 10
- Watch event: 14
- Delete event: 3
- Member event: 1
- Issue comment event: 39
- Push event: 191
- Pull request review event: 73
- Pull request review comment event: 133
- Pull request event: 39
- Fork event: 6
Last Year
- Create event: 12
- Release event: 1
- Issues event: 10
- Watch event: 14
- Delete event: 3
- Member event: 1
- Issue comment event: 39
- Push event: 191
- Pull request review event: 73
- Pull request review comment event: 133
- Pull request event: 39
- Fork event: 6
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 17
- Average time to close issues: about 23 hours
- Average time to close pull requests: 21 days
- Total issue authors: 4
- Total pull request authors: 5
- Average comments per issue: 1.0
- Average comments per pull request: 1.06
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 17
- Average time to close issues: about 23 hours
- Average time to close pull requests: 21 days
- Issue authors: 4
- Pull request authors: 5
- Average comments per issue: 1.0
- Average comments per pull request: 1.06
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jos4uke (2)
- quynhbui1907 (1)
- matthdsm (1)
- mvheetve (1)
Pull Request Authors
- tanyasarkjain (12)
- nf-core-bot (7)
- matthdsm (1)
- sateeshperi (1)
- edmundmiller (1)
- jos4uke (1)
- nvnieuwk (1)
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