bwa_align_stats
short nextflow pipeline to align against a reference genome and produce pile up documents
Science Score: 57.0%
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Low similarity (14.7%) to scientific vocabulary
Repository
short nextflow pipeline to align against a reference genome and produce pile up documents
Basic Info
- Host: GitHub
- Owner: azmigueldario
- License: mit
- Language: Nextflow
- Default Branch: master
- Size: 217 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
azmigueldario/bwaalignstats
Introduction
azmigueldario/bwaalignstats is a bioinformatics pipeline that evaluates the taxonomic classification of isolates (in this case Giardia duodenalis) by aligning against reference genomes. Besides, it will use a high quality reference to produce a pileup format file and do variant calling through different approaches.
Its input are short read fastq files and reference genomes (fasta) as well as parameters to determine optional steps and flags for every module.
Usage
[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.
First, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
csv
sample,fastq_1,fastq_2,organism
SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,
SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,"Pseudomonas_aeruginosa"
Each row represents a fastq file (paired end) with an accompanying sample_id and organism for mapping.
Now, you can run the pipeline using:
bash
nextflow run azmigueldario/bwa_align_stats \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--ref_genome reference_genome_v01.fa.gz \
--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.
Credits
azmigueldario/bwaalignstats was originally written by azmigueldario.
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.
Citations
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: Miguel D Prieto G
- Login: azmigueldario
- Kind: user
- Location: Vancouver, Canada
- Company: Simon Fraser University, CIDGOH
- Repositories: 1
- Profile: https://github.com/azmigueldario
M.D., MSc. Research interests include public health, infectious diseases and molecular epidemiology
Citation (CITATIONS.md)
# azmigueldario/bwa_align_stats: 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 ## 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.
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