{"id":18189942,"url":"https://github.com/kullrich/snpless-nf","last_synced_at":"2026-02-11T17:06:21.483Z","repository":{"id":86806821,"uuid":"432150442","full_name":"kullrich/snpless-nf","owner":"kullrich","description":"snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.","archived":false,"fork":false,"pushed_at":"2024-05-12T21:27:07.000Z","size":106336,"stargazers_count":14,"open_issues_count":1,"forks_count":3,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-08-11T02:36:30.974Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kullrich.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-11-26T11:12:18.000Z","updated_at":"2024-01-09T05:57:11.000Z","dependencies_parsed_at":null,"dependency_job_id":"6225d6ad-e5c7-4062-bdcf-0186366b33c7","html_url":"https://github.com/kullrich/snpless-nf","commit_stats":{"total_commits":108,"total_committers":2,"mean_commits":54.0,"dds":0.25,"last_synced_commit":"c81a7b6c48847db2ace40baa091ee86157ec93d0"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/kullrich/snpless-nf","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fsnpless-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fsnpless-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fsnpless-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fsnpless-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kullrich","download_url":"https://codeload.github.com/kullrich/snpless-nf/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kullrich%2Fsnpless-nf/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29338715,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-11T16:14:43.024Z","status":"ssl_error","status_checked_at":"2026-02-11T16:14:15.258Z","response_time":97,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-03T04:04:38.315Z","updated_at":"2026-02-11T17:06:21.468Z","avatar_url":"https://github.com/kullrich.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ca href=\"https://git.io/typing-svg\"\u003e\u003cimg src=\"https://readme-typing-svg.herokuapp.com?font=Fira+Code\u0026size=30\u0026pause=1000\u0026color=333333\u0026center=true\u0026width=1000\u0026lines=Welcome+to+SNPless+repository+;Ask+me+anything\" alt=\"Typing SVG\" /\u003e\u003c/a\u003e\n\n\u003ch1 align=\"center\"\u003e\u003cb\u003eSNPless powered by \u003cspan style=\"color: green;\"\u003eNextflow\u003c/span\u003e\u003c/b\u003e\u003c/h1\u003e\n\n\nsnpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data. \u003cimg align=\"right\" src=\"logo/new_SNPless.png\" width=400\u003e\n\n[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md)\n[![MITlicense](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)\n[![nextflow](https://img.shields.io/badge/nextflow-%E2%89%A521.10.0-brightgreen.svg)](http://nextflow.io)\n\n## Introduction\n\n## Pipeline summary\n\n1. QC\n    1. FASTQC [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n    2. TRIM [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)\n    3. PEAR [pear](https://cme.h-its.org/exelixis/web/software/pear/)\n2. GENMAP [GenMap](https://github.com/cpockrandt/genmap)\n3. ASSEMBLY\n    1. UNICYCLER [Unicycler](https://github.com/rrwick/Unicycler)\n    2. PROKKA [prokka](https://github.com/tseemann/prokka)\n4. MAPPING\n    1. BRESEQ [breseq](https://github.com/barricklab/breseq) \u003e\u003e SAMTOOLS [samtools](https://github.com/samtools/samtools) add read group\n    2. MINIMAP2 [minimap2](https://github.com/lh3/minimap2) \u003e\u003e SAMBLASTER [samblaster](https://github.com/GregoryFaust/samblaster) remove duplicates\n    3. BWA [BWA](http://bio-bwa.sourceforge.net/) \u003e\u003e SAMBLASTER [samblaster](https://github.com/GregoryFaust/samblaster) remove duplicates\n    4. COVERAGE [samtools](https://github.com/samtools/samtools)\n5. SNPCALLING\n    1. FREEBAYES [freebayes](https://github.com/freebayes/freebayes) \u003e\u003e VCFFILTER [vcflib](https://github.com/vcflib/vcflib) \u003e\u003e VT [Vt](https://genome.sph.umich.edu/wiki/Vt) normalize \u003e\u003e decompose\n    2. BCFTOOLS [bcftools](https://github.com/samtools/bcftools) mpileup, call, vcfutils.pl varFilter \u003e\u003e  VT [Vt](https://genome.sph.umich.edu/wiki/Vt) normalize \u003e\u003e decompose\n    3. LOFREQ [LoFreq](http://csb5.github.io/lofreq/) indelqual, index, call-parallel\n    4. VARSCAN [varscan](http://dkoboldt.github.io/varscan/) mpileup2snp, mpileup2indel\n    5. MPILEUP [samtools](https://github.com/samtools/samtools) \u003e\u003e parse_mpileup.py \u003e\u003e annotate_pvalues\n    6. GDCOMPARE [gdtools](https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html)\n6. SVCALLING\n    1. PINDEL [pindel](https://github.com/genome/pindel)\n    2. GRIDSS [GRIDSS](https://github.com/PapenfussLab/gridss)\n7. FILTERING/MERGING\n    1. BEDTOOLS [bedtools](https://bedtools.readthedocs.io/en/latest/)\n8. ANNOTATION\n    1. SNPEFF [SnpEff](http://pcingola.github.io/SnpEff/)\n9. PLOTTING\n    1. PLOT [R](https://cran.r-project.org/)\n\nAddtional Tools used for data conversion and data analysis:\n\n- HTSLIB [htslib](https://github.com/samtools/htslib)\n- trajectory_pvalue_cpp_code [https://github.com/benjaminhgood/LTEE-metagenomic/tree/master/trajectory_pvalue_cpp_code](https://github.com/benjaminhgood/LTEE-metagenomic/tree/master/trajectory_pvalue_cpp_code) compiled into annotate_pvalues\n- create_timecourse.py [https://github.com/benjaminhgood/LTEE-metagenomic/blob/master/cluster_scripts/create_timecourse.py](https://github.com/benjaminhgood/LTEE-metagenomic/blob/master/cluster_scripts/create_timecourse.py) used in parse_mpileup.py\n\n## Quickstart\n\n1. Install [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) (\u003e=21.10.0)\n\nInstall Nextflow by using the following command:\n\n```\ncurl -s https://get.nextflow.io | bash\n```\n\nor\n\nInstall Nextflow by using conda:\n\n```\nconda create -n nf python=3\nconda activate nf\nconda install -c bioconda nextflow\n```\n\n2. Download the pipeline\n\n```\ngit clone https://github.com/kullrich/snpless-nf.git\n```\n\n3. Test the pipeline on an minimal dataset with a single command:\n\nUsing nextflow conda environment:\n\n```\nconda activate nf\nnextflow run snpless-nf -profile test\n```\n\n4. Start running your own analysis:\n\nCheck the necessary input files!\n\n```\nnextflow run snpless-nf --input \u003csamples.tsv\u003e --reference \u003cgenome.fna\u003e --gff3 \u003cgenome.gff3\u003e --proteins \u003cgenome.gbff\u003e\n```\n\n## Full example dataset\n\n### Get example files (8.6 GB)\n\nDownload via wget:\n\n```\ncd snpless-nf/examples\nwget -O behringer2018.tar.gz https://owncloud.gwdg.de/index.php/s/fqD9ik2s3FReOUn/download\ntar -xvf behringer2018.tar.gz\n```\n\nDownload via weblink:\n\n[behringer2018 - samples 113, 129, 221](https://ftp.evolbio.mpg.de/main.html?download\u0026weblink=74b3a1f98426435d16a97bcc8e55b400\u0026realfilename=behringer2018.tar.gz)\n\n### Run full example dataset\n\nUsing nextflow conda environment:\n\n```\nconda activate nf\nnextflow run snpless-nf --input behringer2018/behringer2018_113.txt --reference behringer2018/GCF_000005845.2_ASM584v2_genomic.fna --gff3 GCF_000005845.2_ASM584v2_genomic.gff --proteins behringer2018/GCF_000005845.2_ASM584v2_genomic.gbff\n```\n\n## Pipeline usage\n\nsee a detailed description here: [usage](https://github.com/kullrich/snpless-nf/blob/main/docs/usage.md)\n\n### Input files\n\n## Pipeline parameters\n\nsee a detailed description here: [parameters](https://github.com/kullrich/snpless-nf/blob/main/docs/parameters.md)\n\n## Pipeline output\n\nsee a detailed description here: [output](https://github.com/kullrich/snpless-nf/blob/main/docs/output.md)\n\n## Licence\n\nMIT (see LICENSE)\n\n## Contributing Code\n\nIf you would like to contribute to snpless-nf, please file an issue so that one can establish a statement of need, avoid redundant work, and track progress on your contribution.\n\nBefore you do a pull request, you should always file an issue and make sure that someone from the snpless-nf developer team agrees that it’s a problem, and is happy with your basic proposal for fixing it.\n\nOnce an issue has been filed and we've identified how to best orient your contribution with package development as a whole, [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) the [main repo](https://github.com/kullrich/snpless-nf.git), branch off a [feature branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) from `master`, [commit](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/committing-and-reviewing-changes-to-your-project) and [push](https://docs.github.com/en/github/using-git/pushing-commits-to-a-remote-repository) your changes to your fork and submit a [pull request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/proposing-changes-to-your-work-with-pull-requests) for `snpless-nf:master`.\n\nBy contributing to this project, you agree to abide by the Code of Conduct terms.\n\n## Bug reports\n\nPlease report any errors or requests regarding [snpless-nf](https://github.com/kullrich/snpless-nf) to Kristian Ullrich (ullrich@evolbio.mpg.de)\n\n## Code of Conduct - Participation guidelines\n\nThis repository adhere to [Contributor Covenant](http://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/snpless-nf/-/blob/master/CODE_OF_CONDUCT.md))\n\nSee also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf).\n\nBy contributing to this project, you agree to abide by its terms.\n\n## References - Examples\n\nBehringer, Megan G., et al. \"Escherichia coli cultures maintain stable subpopulation structure during long-term evolution.\" Proceedings of the National Academy of Sciences 115.20 (2018): E4642-E4650. [https://www.pnas.org/content/115/20/E4642.short](https://www.pnas.org/content/115/20/E4642.short)\n\n## References - Tools\n1. Good, Benjamin H., et al. \"The dynamics of molecular evolution over 60,000 generations.\" Nature 551.7678 (2017): 45-50. [link](https://www.nature.com/articles/nature24287)\n2. Di Tommaso, Paolo, et al. \"Nextflow enables reproducible computational workflows.\" Nature biotechnology 35.4 (2017): 316-319. [link](https://www.nature.com/articles/nbt.3820?report=reader)\n3. Andrews, Simon. \"FastQC: a quality control tool for high throughput sequence data. 2010.\" (2017): W29-33. [link](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n4.Bolger, Anthony M., Marc Lohse, and Bjoern Usadel. \"Trimmomatic: a flexible trimmer for Illumina sequence data.\" Bioinformatics 30.15 (2014): 2114-2120. [link](https://academic.oup.com/bioinformatics/article/30/15/2114/2390096?login=true)\n5. Zhang, Jiajie, et al. \"PEAR: a fast and accurate Illumina Paired-End reAd mergeR.\" Bioinformatics 30.5 (2014): 614-620. [link](https://academic.oup.com/bioinformatics/article/30/5/614/247231?login=true)\n6. Pockrandt, Christopher, et al. \"GenMap: ultra-fast computation of genome mappability.\" Bioinformatics 36.12 (2020): 3687-3692. [link](https://academic.oup.com/bioinformatics/article/36/12/3687/5815974?login=true)\n7. Wick, Ryan R., et al. \"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads.\" PLoS computational biology 13.6 (2017): e1005595. [link](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595)\n8. Seemann, Torsten. \"Prokka: rapid prokaryotic genome annotation.\" Bioinformatics 30.14 (2014): 2068-2069. [link](https://academic.oup.com/bioinformatics/article/30/14/2068/2390517?login=true)\n9. Deatherage, Daniel E., and Jeffrey E. Barrick. \"Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.\" Engineering and analyzing multicellular systems. Humana Press, New York, NY, 2014. 165-188. [link](https://link.springer.com/content/pdf/10.1007/978-1-4939-0554-6_12.pdf)\n10. Li, Heng. \"Minimap2: pairwise alignment for nucleotide sequences.\" Bioinformatics 34.18 (2018): 3094-3100. [link](https://academic.oup.com/bioinformatics/article/34/18/3094/4994778?login=true)\n11. Li, Heng. \"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.\" arXiv preprint arXiv:1303.3997 (2013). [link](https://arxiv.org/abs/1303.3997)\n12. Faust, Gregory G., and Ira M. Hall. \"SAMBLASTER: fast duplicate marking and structural variant read extraction.\" Bioinformatics 30.17 (2014): 2503-2505. [link](https://academic.oup.com/bioinformatics/article/30/17/2503/2748175?login=true)\n13. Li, Heng, et al. \"The sequence alignment/map format and SAMtools.\" Bioinformatics 25.16 (2009): 2078-2079. [link](https://academic.oup.com/bioinformatics/article/25/16/2078/204688?login=true)\n14. Garrison, Erik, and Gabor Marth. \"Haplotype-based variant detection from short-read sequencing.\" arXiv preprint arXiv:1207.3907 (2012). [link](https://arxiv.org/abs/1207.3907)\n15. Wilm, Andreas, et al. \"LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.\" Nucleic acids research 40.22 (2012): 11189-11201. [link](https://academic.oup.com/nar/article/40/22/11189/1152727?login=true)\n16. Koboldt, Daniel C., et al. \"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.\" Genome research 22.3 (2012): 568-576. [link](https://genome.cshlp.org/content/22/3/568.short)\n17. Ye, Kai, et al. \"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.\" Bioinformatics 25.21 (2009): 2865-2871. [link](https://academic.oup.com/bioinformatics/article/25/21/2865/2112044?login=true)\n18. Cameron, Daniel L., et al. \"GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.\" bioRxiv (2021): 2020-07. [link](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02423-x)\n19. Quinlan, Aaron R., and Ira M. Hall. \"BEDTools: a flexible suite of utilities for comparing genomic features.\" Bioinformatics 26.6 (2010): 841-842. [link](https://academic.oup.com/bioinformatics/article/26/6/841/244688?login=true)\n20. Cingolani, Pablo, et al. \"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.\" Fly 6.2 (2012): 80-92. [link](https://www.tandfonline.com/doi/full/10.4161/fly.19695)\n21. Wickham, Hadley. \"ggplot2.\" Wiley Interdisciplinary Reviews: Computational Statistics 3.2 (2011): 180-185. 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