hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
Science Score: 67.0%
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Low similarity (11.5%) to scientific vocabulary
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Repository
A pipeline to investigate horizontal gene transfer from NGS data
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: master
- Homepage: https://nf-co.re/hgtseq
- Size: 5.12 MB
Statistics
- Stars: 26
- Watchers: 169
- Forks: 7
- Open Issues: 2
- Releases: 2
Topics
Metadata Files
README.md
Introduction
nf-core/hgtseq is a bioinformatics best-practice analysis pipeline built to investigate horizontal gene transfer from NGS data.
The pipeline uses metagenomic classification of paired-read alignments against a reference genome to identify the presence of non-host microbial sequences within read pairs, and to infer potential integration sites into the host genome.
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!
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.
Functionality Overview
A graphical view of the pipeline can be seen below.
Pipeline summary
- Read QC (
FastQC) - Present QC for raw reads (
MultiQC) - Adapter and quality trimming (
Trim Galore) - Mapping reads using BWA (
BWA) - Sort and index alignments, extraction reads by sam flag and conversion to fastq format(
SAMtools) - Taxonomic classification (
Kraken2) - Plotting Kraken2 results (
Krona) - Html analysis report (
RMarkDown)
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.
console
nextflow run nf-core/hgtseq \
--input <YOURINPUT>.csv \
--outdir <OUTDIR> \
--genome GRCh38 \
--taxonomy_id "TAXID" \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
--krakendb /path/to/kraken_db \
--kronadb /path/to/krona_db/taxonomy.tab
bash
nextflow run nf-core/hgtseq \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>
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.
For more details, please refer to the usage documentation and the parameter documentation.
Pipeline output
To see the the results of a 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/hgtseq was originally written by Simone Carpanzano, Francesco Lescai.
We thank nf-core community, and in particular the authors of the modules used in the pipeline: Paolo Cozzi, Jose Espinosa-Carrasco, Phil Ewels, Gisela Gabernet, Maxime Garcia, Jeremy Guntoro, Friederike Hanssen, Matthias Hortenhuber, Patrick Hüther, Suzanne Jin, Felix Krueger, Harshil Patel, Alex Peltzer, Abhinav Sharma, Gregor Sturm, James Fellows Yates.
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 #hgtseq channel (you can join with this invite).
Citations
If you use nf-core/hgtseq for your analysis, please cite it using the following doi: 10.5281/zenodo.7244734
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/hgtseq: Citations ## [hgtseq](https://www.mdpi.com/1422-0067/23/23/14512) > Carpanzano S, Santorsola M, Nf-Core Community, Lescai F. hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer. Int J Mol Sci. 2022 Nov 22;23(23):14512. doi: 10.3390/ijms232314512. PMID: 36498841; PMCID: PMC9738810. ## [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/) - [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. - [Trim Galore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) - [Qualimap](http://qualimap.conesalab.org) > Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2015). “Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.” Bioinformatics, btv566 - [BAMTOOLS](https://github.com/pezmaster31/bamtools) > Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14. PubMed PMID: 21493652; PubMed Central PMCID: PMC3106182. - [BWA](http://bio-bwa.sourceforge.net) > Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997. - [BWAmem2](https://github.com/bwa-mem2/bwa-mem2) > Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. - [SAMtools](https://www.htslib.org) > 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. - [Kraken2](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown) > Wood, Derrick E., Jennifer Lu, and Ben Langmead. (2019). Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0. - [Krona](https://hpc.nih.gov/apps/kronatools.html) > Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC bioinformatics, 12(1), 1-10. doi: 10.1186/1471-2105-12-385. - [RMarkDown](https://rmarkdown.rstudio.com) > Yihui Xie and J.J. Allaire and Garrett Grolemund (2018). R Markdown: The Definitive Guide. Chapman and Hall/CRC. ISBN 9781138359338. URL https://bookdown.org/yihui/rmarkdown. ## 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) - [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
- Issues event: 1
- Watch event: 7
- Issue comment event: 5
- Push event: 5
- Pull request event: 11
- Fork event: 3
- Create event: 6
Last Year
- Issues event: 1
- Watch event: 7
- Issue comment event: 5
- Push event: 5
- Pull request event: 11
- Fork event: 3
- Create event: 6
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carpanzano | s****1@u****t | 210 |
| Francesco L | f****i@u****t | 107 |
| Simone Carpanzano | 9****z@u****m | 27 |
| nf-core-bot | c****e@n****e | 7 |
| Francesco Lescai | 5****i@u****m | 5 |
| Maxime U. Garcia | m****a@s****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 4
- Total pull requests: 37
- Average time to close issues: 3 months
- Average time to close pull requests: 15 days
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 0.25
- Average comments per pull request: 1.24
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: about 2 months
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.5
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lescai (1)
- microbemarsh (1)
- carpanz (1)
- jen-reeve (1)
Pull Request Authors
- nf-core-bot (21)
- carpanz (20)
- lescai (3)
- maxulysse (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- nf-core/tower-action v3 composite
- nf-core/tower-action v3 composite
- mshick/add-pr-comment v1 composite
- actions/checkout v2 composite
- nf-core/setup-nextflow v1 composite
- actions/checkout v3 composite
- actions/setup-node v2 composite
- actions/checkout v2 composite
- actions/setup-node v2 composite
- actions/setup-python v3 composite
- actions/upload-artifact v2 composite
- mshick/add-pr-comment v1 composite
- nf-core/setup-nextflow v1 composite
- psf/black stable composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/stale v7 composite