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**nf-core/eager** is a bioinformatics pipeline that ...
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**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.
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<!-- TODO nf-core:
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Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
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major pipeline sections and the types of output it produces. You're giving an overview to someone new
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to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
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-->
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## Pipeline summary
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<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
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workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->
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<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
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- (Optionally) create reference genome indices for mapping (`bwa`, `samtools`, and `picard`)
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- Sequencing quality control (`FastQC`, `Falco`)
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- Sequencing adapter removal, paired-end data merging (`AdapterRemoval`)
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- Read mapping to reference using (`bwa aln`, `bwa mem`, `CircularMapper`, `bowtie2`, or `mapAD`)
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- Post-mapping processing, statistics and conversion to bam (`samtools`, and `preseq`)
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- Ancient DNA C-to-T damage pattern visualisation (`DamageProfiler`)
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- PCR duplicate removal (`DeDup` or `MarkDuplicates`)
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- Post-mapping statistics and BAM quality control (`Qualimap`)
- Post-AdapterRemoval trimming of FASTQ files prior mapping (`fastp`)
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- Automatic conversion of unmapped reads to FASTQ (`samtools`)
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- Host DNA (mapped reads) stripping from input FASTQ files (for sensitive samples)
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#### aDNA Damage manipulation
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- Damage removal/clipping for UDG+/UDG-half treatment protocols (`BamUtil`)
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- Damaged reads extraction and assessment (`PMDTools`)
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- Nuclear DNA contamination estimation of human samples (`angsd`)
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#### Genotyping
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- Creation of VCF genotyping files (`GATK UnifiedGenotyper`, `GATK HaplotypeCaller` and `FreeBayes`)
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- Creation of EIGENSTRAT genotyping files (`pileupCaller`)
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- Creation of Genotype Likelihood files (`angsd`)
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- Consensus sequence FASTA creation (`VCF2Genome`)
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- SNP Table generation (`MultiVCFAnalyzer`)
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#### Biological Information
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- Mitochondrial to Nuclear read ratio calculation (`MtNucRatioCalculator`)
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- Statistical sex determination of human individuals (`Sex.DetERRmine`)
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#### Metagenomic Screening
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- Low-sequenced complexity filtering (`BBduk` or `PRINSEQ++`)
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- Taxonomic binner with alignment (`MALT` or `MetaPhlAn 4`)
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- Taxonomic binner without alignment (`Kraken2`,`KrakenUniq`)
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- aDNA characteristic screening of taxonomically binned data from MALT (`MaltExtract`)
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#### Functionality Overview
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A graphical overview of suggested routes through the pipeline depending on context can be seen below.
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<palign="center">
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<img src="docs/images/eager2_metromap_complex.png" alt="nf-core/eager metro map" width="70%"
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</p>
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## Usage
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> [!NOTE]
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> 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.
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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
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Explain what rows and columns represent. For instance (please edit as appropriate):
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First, prepare a samplesheet with your input data that looks as follows:
sample1 sample1_a 1 4 paired double none /<path>/<to>/sample1_a_l1_r1.fq.gz /<path>/<to>/sample1_a_l1_r2.fq.gz NA NA
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sample2 sample2_a 2 2 single double full /<path>/<to>/sample2_a_l1_r1.fq.gz NA NA NA
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sample3 sample3_a 8 4 single double half NA NA /<path>/<to>/sample31_a.bam Mammoth_MT_Krause
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```
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Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
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-->
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Each row represents a fastq file (single-end), pair of fastq files (paired end), and/or a bam file.
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Now, you can run the pipeline using:
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<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
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```bash
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nextflow run nf-core/eager \
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-profile <docker/singularity/.../institute> \
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--input samplesheet.csv \
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--fasta '<your_reference>.fasta' \
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--outdir <OUTDIR>
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```
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@@ -76,11 +128,40 @@ For more details about the output files and reports, please refer to the
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## Credits
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nf-core/eager was originally written by The nf-core/eager community.
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This 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 Fagernäs](https://github.com/ZandraFagernas), [Aida Andrades Valtueña](https://github.com/aidaanva) and [Maxime Garcia](https://github.com/MaxUlysse) and the nf-core community.
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We thank the following people for their extensive assistance in the development of this pipeline:
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<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
@@ -90,10 +171,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
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## Citations
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<!-- 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. -->
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<!-- If you use nf-core/eager for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
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If you use nf-core/eager for your analysis, please cite it using the following doi:
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<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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> Fellows Yates JA, Lamnidis TC, Borry M, Valtueña Andrades A, Fagernäs 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).
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An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
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