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"@id": "./",
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"@type": "Dataset",
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"creativeWorkStatus": "InProgress",
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"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core_eager_logo_outline_drop.png\">\n <img alt=\"nf-core/eager\" src=\"docs/images/nf-core_eager_logo_outline_drop.png\">\n </picture>\n</h1>\n\n[](https://github.com/codespaces/new/nf-core/eager)\n[](https://github.com/nf-core/eager/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/eager/actions/workflows/linting.yml)[](https://nf-co.re/eager/results)[](https://doi.org/10.5281/zenodo.1465061)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/eager)\n\n[](https://nfcore.slack.com/channels/eager)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n\n\n## Introduction\n\n**nf-core/eager** is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.\n\n## Pipeline summary\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n- (Optionally) create reference genome indices for mapping (`bwa`, `samtools`, and `picard`)\n- Sequencing quality control (`FastQC`, `Falco`)\n- Sequencing adapter removal, paired-end data merging (`AdapterRemoval`)\n- Read mapping to reference using (`bwa aln`, `bwa mem`, `CircularMapper`, `bowtie2`, or `mapAD`)\n- Post-mapping processing, statistics and conversion to bam (`samtools`, and `preseq`)\n- Ancient DNA C-to-T damage pattern visualisation (`DamageProfiler`)\n- PCR duplicate removal (`DeDup` or `MarkDuplicates`)\n- Post-mapping statistics and BAM quality control (`Qualimap`)\n- Library Complexity Estimation (`preseq`)\n- Overall pipeline statistics summaries (`MultiQC`)\n\n### Additional Steps\n\nAdditional functionality contained by the pipeline currently includes:\n\n#### Input\n\n- Automatic merging of complex sequencing setups (e.g. multiple lanes, sequencing configurations, library types)\n\n#### Preprocessing\n\n- Illumina two-coloured sequencer poly-G tail removal (`fastp`)\n- Post-AdapterRemoval trimming of FASTQ files prior mapping (`fastp`)\n- Automatic conversion of unmapped reads to FASTQ (`samtools`)\n- Host DNA (mapped reads) stripping from input FASTQ files (for sensitive samples)\n\n#### aDNA Damage manipulation\n\n- Damage removal/clipping for UDG+/UDG-half treatment protocols (`BamUtil`)\n- Damaged reads extraction and assessment (`PMDTools`)\n- Nuclear DNA contamination estimation of human samples (`angsd`)\n\n#### Genotyping\n\n- Creation of VCF genotyping files (`GATK UnifiedGenotyper`, `GATK HaplotypeCaller` and `FreeBayes`)\n- Creation of EIGENSTRAT genotyping files (`pileupCaller`)\n- Creation of Genotype Likelihood files (`angsd`)\n- Consensus sequence FASTA creation (`VCF2Genome`)\n- SNP Table generation (`MultiVCFAnalyzer`)\n\n#### Biological Information\n\n- Mitochondrial to Nuclear read ratio calculation (`MtNucRatioCalculator`)\n- Statistical sex determination of human individuals (`Sex.DetERRmine`)\n\n#### Metagenomic Screening\n\n- Low-sequenced complexity filtering (`BBduk` or `PRINSEQ++`)\n- Taxonomic binner with alignment (`MALT` or `MetaPhlAn 4`)\n- Taxonomic binner without alignment (`Kraken2`,`KrakenUniq`)\n- aDNA characteristic screening of taxonomically binned data from MALT (`MaltExtract`)\n\n#### Functionality Overview\n\nA graphical overview of suggested routes through the pipeline depending on context can be seen below.\n\n<p align=\"center\">\n <img src=\"docs/images/eager2_metromap_complex.png\" alt=\"nf-core/eager metro map\" width=\"70%\"\n</p>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.tsv`:\n\n```csv\nample_id\tlibrary_id\tlane\tcolour_chemistry\tpairment\tstrandedness\tdamage_treatment\tr1\tr2\tbam\tbam_reference_id\nsample1\tsample1_a\t1\t4\tpaired\tdouble\tnone\t/<path>/<to>/sample1_a_l1_r1.fq.gz /<path>/<to>/sample1_a_l1_r2.fq.gz\tNA\tNA\nsample2\tsample2_a\t2\t2\tsingle\tdouble\tfull\t/<path>/<to>/sample2_a_l1_r1.fq.gz\tNA\tNA\tNA\nsample3\tsample3_a\t8\t4\tsingle\tdouble\thalf\tNA\tNA\t/<path>/<to>/sample31_a.bam\tMammoth_MT_Krause\n```\n\nEach row represents a fastq file (single-end), pair of fastq files (paired end), and/or a bam file.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/eager \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --fasta '<your_reference>.fasta' \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/eager/usage) and the [parameter documentation](https://nf-co.re/eager/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/eager/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/eager/output).\n\n## Credits\n\nThis pipeline was established by Alexander Peltzer ([apeltzer](https://github.com/apeltzer)) and [James A. Fellows Yates](https://github.com/jfy133). Version two had major contributions from [Stephen Clayton](https://github.com/sc13-bioinf), [Thiseas C. Lamnidis](https://github.com/TCLamnidis), [Maxime Borry](https://github.com/maxibor), [Zandra Fagern\u00e4s](https://github.com/ZandraFagernas), [Aida Andrades Valtue\u00f1a](https://github.com/aidaanva) and [Maxime Garcia](https://github.com/MaxUlysse) and the nf-core community.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Alex H\u00fcbner](https://github.com/alexhbnr)\n- [Alexandre Gilardet](https://github.com/alexandregilardet)\n- Arielle Munters\n- [\u00c5shild V\u00e5gene](https://github.com/ashildv)\n- [Charles Plessy](https://github.com/charles-plessy)\n- [Elina Salmela](https://github.com/esalmela)\n- [Fabian Lehmann](https://github.com/Lehmann-Fabian)\n- [He Yu](https://github.com/paulayu)\n- [Hester van Schalkwyk](https://github.com/hesterjvs)\n- [Ian Light-M\u00e1ka](https://github.com/ilight1542)\n- [Ido Bar](https://github.com/IdoBar)\n- [Irina Velsko](https://github.com/ivelsko)\n- [I\u015f\u0131n Alt\u0131nkaya](https://github.com/isinaltinkaya)\n- [Johan Nylander](https://github.com/nylander)\n- [Jonas Niemann](https://github.com/NiemannJ)\n- [Katerine Eaton](https://github.com/ktmeaton)\n- [Kathrin N\u00e4gele](https://github.com/KathrinNaegele)\n- [Kevin Lord](https://github.com/lordkev)\n- [Luc Venturini](https://github.com/lucventurini)\n- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)\n- [Marcel Keller](https://github.com/marcel-keller)\n- [Megan Michel](https://github.com/meganemichel)\n- [Merlin Szymanski](https://github.com/merszym)\n- [Pierre Lindenbaum](https://github.com/lindenb)\n- [Pontus Skoglund](https://github.com/pontussk)\n- [Raphael Eisenhofer](https://github.com/EisenRa)\n- [Roberta Davidson](https://github.com/roberta-davidson)\n- [Rodrigo Barquera](https://github.com/RodrigoBarquera)\n- [Selina Carlhoff](https://github.com/scarlhoff)\n- [Torsten G\u00fcnter](https://bitbucket.org/tguenther)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#eager` channel](https://nfcore.slack.com/channels/eager) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/eager for your analysis, please cite it using the following doi:\n\n> Fellows Yates JA, Lamnidis TC, Borry M, Valtue\u00f1a Andrades A, Fagern\u00e4s Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947. DOI: [10.7717/peerj.10947](https://doi.org/10.7717/peerj.10947).\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
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