{"id":41035033,"url":"https://github.com/maxibor/adnamap","last_synced_at":"2026-01-22T10:31:58.966Z","repository":{"id":51561565,"uuid":"503114073","full_name":"maxibor/adnamap","owner":"maxibor","description":"aDNA mapping to multiple genomes","archived":false,"fork":false,"pushed_at":"2025-02-04T15:38:46.000Z","size":31467,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-17T09:42:33.616Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","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/maxibor.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-06-13T21:02:17.000Z","updated_at":"2025-01-09T15:07:50.000Z","dependencies_parsed_at":"2025-09-05T14:48:23.382Z","dependency_job_id":null,"html_url":"https://github.com/maxibor/adnamap","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/maxibor/adnamap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fadnamap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fadnamap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fadnamap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fadnamap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/maxibor","download_url":"https://codeload.github.com/maxibor/adnamap/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fadnamap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28661874,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2026-01-22T10:31:58.872Z","updated_at":"2026-01-22T10:31:58.948Z","avatar_url":"https://github.com/maxibor.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# aDNAMap\n\n**adnamap** is a bioinformatics best-practice analysis pipeline for aDNA mapping to mulitple genomes.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), 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](https://www.nextflow.io/docs/latest/dsl2.html) 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](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n\u003c!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable --\u003e\n\nOn 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](https://nf-co.re/adnamap/results).\n\n## Pipeline summary\n\n\u003c!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline --\u003e\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Quick Start\n\n1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`\u003e=21.10.3`)\n\n2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.\n\n3. Download the pipeline and test it on a minimal dataset with a single command:\n\n   ```console\n   nextflow run nf-core/adnamap -profile test,YOURPROFILE --outdir \u003cOUTDIR\u003e\n   ```\n\n   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.\n\n   \u003e - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.\n   \u003e - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile \u003cinstitute\u003e` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.\n   \u003e - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.\n   \u003e - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.\n\n4. Start running your own analysis!\n\n\n   ```console\n   nextflow run nf-core/adnamap --input samplesheet.csv  --genomes genome_sheet.csv --outdir \u003cOUTDIR\u003e -profile \u003cdocker/singularity/podman/shifter/charliecloud/conda/institute\u003e\n   ```\n\n## Documentation\n\nThe adnamap pipeline comes with documentation about the pipeline [usage](docs/usage), [parameters](docs/parameters) and [output](docs/output).\n\n## Credits\n\nnf-core/adnamap was originally written by Maxime Borry.\n## Pipeline workflow\n\n```mermaid\nflowchart TD\n    subgraph fastq_process[FastQ preprocessing]\n        fastq{FastQ file}\n        fastqc_before[FastQC before]\n        fastp[\"fastp: \\n Adapter and Quality trimming + merging + deduplication\"]\n        fastqc_after[FastQC after]\n        fastq --\u003e fastqc_before\n        fastq --\u003e fastp\n        fastp -- Trimmed fastq --\u003e fastqc_after\n    end\n    subgraph fastq_preproprecessing[FastA preprocessing]\n        fasta{Genome FastA file}\n        faidx[Samtools faidx]\n        fasta --compressed--\u003egunzip\n        gunzip--\u003ebowtie2_build\n        bowtie2_build[Bowtie2-build]\n        fasta--not compressed--\u003e bowtie2_build\n        gunzip--\u003efaidx\n        fasta--not compressed--\u003efaidx\n    end\n    subgraph alignment[Alignment]\n        bowtie2_align[\"Bowtie2 align subworkflow\"]\n        bowtie2_build --Bowtie 2 index--\u003e bowtie2_align\n        fastp --Trimmed fastq--\u003e bowtie2_align\n    end\n    subgraph lca[LCA]\n      bowtie2_align --samtools merge--\u003e merged_BAM[\"Merged BAM per sample\"]\n      merged_BAM --sam2lca--\u003e rank_BAM[\"taxon rank specific BAM\"]\n    end\n    subgraph alignment_post[Alignment post_processing]\n        qualimap[Alignment stats reporting]\n        damageprofiler[DamageProfiler: aDNA stats]\n        fasta--decompressed--\u003edamageprofiler\n        gunzip--\u003edamageprofiler\n        rank_BAM--BAM+index--\u003edamageprofiler\n        rank_BAM--BAM+index--\u003equalimap\n    end\n    subgraph variant_calling[Variant calling]\n        snpAD[\"snpAD: ancient DNA damage aware genotyper\"]\n        freebayes[\"Freebayes: genotyper\"]\n\n        rank_BAM--BAM+index--\u003esnpAD\n        rank_BAM--BAM+index--\u003efreebayes\n        fasta--decompressed--\u003esnpAD\n        gunzip--\u003efreebayes\n        faidx--\u003efreebayes\n        fasta--decompressed--\u003esnpAD\n        gunzip--\u003efreebayes\n        faidx--\u003esnpAD\n        vcf{VCF}\n        freebayes --\u003e vcf\n        vcf-- bcftools consensus --\u003econs_fa[\"Consensus genome fasta\"]\n    end\n```\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\u003c!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --\u003e\n\u003c!-- If you use  nf-core/adnamap for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\n\u003c!-- TODO nf-core: Add bibliography of tools and data used in your pipeline --\u003e\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline integrates code templates and was made with tools from the [`nf-core` community](https://nf-co.re/). More in their publication below:\n\n\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fadnamap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxibor%2Fadnamap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fadnamap/lists"}