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"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-seqinspector_logo_dark.png\">\n <img alt=\"nf-core/seqinspector\" src=\"docs/images/nf-core-seqinspector_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/codespaces/new/nf-core/seqinspector)\n[](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[](https://nf-co.re/seqinspector/results)[](https://doi.org/10.5281/zenodo.18757486)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.1.0)\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/seqinspector)\n\n[](https://nfcore.slack.com/channels/seqinspector)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that processes raw sequence data (FASTQ) to provide comprehensive quality control.\nIt can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants.\nThe pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.\nIf provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.\n\n### Compatibility between tools and data type\n\n<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->\n\n| Tool Type | Tool Name | Tool Description | Compatibility with Data | Dependencies | Default tool |\n| -------------------------- | ------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------ | ----------------------- | ---------------------------------------------------------------------------------------- | ------------ |\n| `Subsampling` | [`Seqtk`](https://github.com/lh3/seqtk) | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA] | [N/A] | no |\n| `Lint FASTQs` | [`fq`](https://github.com/stjude-rust-labs/fq) | fq filters, generates, subsamples, and validates FASTQ files. | [RNA, DNA, synthetic] | [N/A] | yes |\n| `Trimming` | [`Chelae`](https://github.com/fulcrumgenomics/chelae) | Adapter and quality trimming of short-read FASTQ data. | [RNA, DNA, synthetic] | [N/A] | no |\n| `Trimming` | [`Fastp`](https://github.com/OpenGene/fastp) | Trimming of reads. Only performs trimming if `--tools` parameter is given. | [RNA, DNA, synthetic] | [N/A] | no |\n| `Deduplication assessment` | [`BBMap Clumpify`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/) | Deduplicate and compress FASTQ files. Only performs clumpify if `--tools` parameter is given. | [RNA, DNA] | [N/A] | no |\n| `Indexing, Mapping` | [`BWA-MEM2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] | yes |\n| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] | yes |\n| `QC` | [`checkQC`](https://github.com/Molmed/checkQC) | Read QC | [RNA, DNA] | Illumina rundir | no |\n| `QC` | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Read QC | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`FASTQE`](https://fastqe.com/) | Read QC | [RNA, DNA] | [N/A] | no |\n| `QC` | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) | Basic contamination detection | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`SeqFu Stats`](https://github.com/telatin/seqfu2) | Sequence statistics | [RNA, DNA] | [N/A] | yes |\n| `QC` | [`Seqkit Stats`](https://bioinf.shenwei.me/seqkit/usage/#stats) | Simple statistics of FASTA/Q files | [RNA, DNA] | [N/A] | no |\n| `QC` | [`Sequali`](https://sequali.readthedocs.io/en/latest/) | Read QC for long and short reads. | [RNA, DNA] | [N/A] | yes |\n| `Taxonomic Classification` | [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) | Performs taxonomic classification and/or profiling | [RNA, DNA] | [N/A] | no |\n| `QC` | [`Picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [BWA-MEM2, SAMtools, `--genome`] | yes |\n| `QC` | [`Picard CollectHsMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data. | [RNA, DNA] | [BWA-MEM2, SAMtools, `--fasta`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no |\n| `QC` | [`Riker`](https://github.com/fulcrumgenomics/riker) | Collect BAM-level QC metrics (alignment, base distribution, insert size, GC bias, WGS, error metrics). | [DNA] | [BWA-MEM2, SAMtools, `--fasta`] | no |\n| `Reporting` | [`MultiQC`](http://multiqc.info/) | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] | yes |\n| `Reporting` | [`Krona`](https://hpc.nih.gov/apps/kronatools.html) | Plotting Kraken2 results | [RNA, DNA, synthetic] | [kraken2] | no |\n\n### Workflow diagram\n\nThe subway map below is a graphical representation of the pipeline workflow, generated with [nf-metro](https://seqeralabs.github.io/nf-metro/).\n\n<picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_tubemap_dark.png\">\n <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_tubemap_light.png\">\n <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_tubemap_light.png\">\n</picture>\n\nThe diagram below illustrates the MultiQC reporting logic for per-sample tags and global aggregation.\n\n<picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/seqinspector_multiqc_dark.png\">\n <source media=\"(prefers-color-scheme: light)\" srcset=\"docs/images/seqinspector_multiqc_light.png\">\n <img alt=\"Fallback image description\" src=\"docs/images/seqinspector_multiqc_light.png\">\n</picture>\n\n### Summary of tools and version used in the pipeline\n\n| Tool | Version |\n| ----------- | ------- |\n| bwamem2 | 2.3 |\n| bbmap | 39.18 |\n| checkQC | 4.1.0 |\n| chelae | 0.1.0 |\n| fq/lint | 0.12.0 |\n| fastp | 1.3.6 |\n| fastqc | 0.12.1 |\n| fastqe | 0.5.2 |\n| fastqscreen | 0.16.0 |\n| kraken2 | 2.1.6 |\n| krona | 2.8.1 |\n| multiqc | 1.35 |\n| multiqcsav | 0.2.0 |\n| picard | 3.4.0 |\n| riker | 0.4.0 |\n| samtools | 1.24 |\n| seqfu | 1.22.3 |\n| seqkit | 2.9.0 |\n| seqtk | 1.4 |\n| sequali | 1.0.2 |\n| toulligqc | 2.8.4 |\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-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.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`).\n`rundir` is the path to the runfolder.\n`tags` is a colon-separated list of tags that will be added to the MultiQC report for this `sample`.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/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/seqinspector/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/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by [@agrima2010](https://github.com/agrima2010), [@Aratz](https://github.com/Aratz), [@FranBonath](https://github.com/FranBonath), [@kedhammar](https://github.com/kedhammar), and [@MatthiasZepper](https://github.com/MatthiasZepper) from the Swedish [National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).\n\nMaintenance is now lead by Maxime U Garcia ([National Genomics Infrastructure](https://github.com/NationalGenomicsInfrastructure/))\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@adamrtalbot](https://github.com/adamrtalbot)\n- [@alneberg](https://github.com/alneberg)\n- [@beatrizsavinhas](https://github.com/beatrizsavinhas)\n- [@ctuni](https://github.com/ctuni)\n- [@edmundmiller](https://github.com/edmundmiller)\n- [@EliottBo](https://github.com/EliottBo)\n- [@erkutilaslan](https://github.com/erkutilaslan)\n- [@KarNair](https://github.com/KarNair)\n- [@kjellinjonas](https://github.com/kjellinjonas)\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n- [@matrulda](https://github.com/matrulda)\n- [@mirpedrol](https://github.com/mirpedrol)\n- [@nggvs](https://github.com/nggvs)\n- [@nkongenelly](https://github.com/nkongenelly)\n- [@Patricie34](https://github.com/Patricie34)\n- [@pontushojer](https://github.com/pontushojer)\n- [@ramprasadn](https://github.com/ramprasadn)\n- [@rannick](https://github.com/rannick)\n- [@sarajeeeze](https://github.com/sarajeeeze)\n- [@TMAdams](https://github.com/TMAdams)\n- [@torigiffin](https://github.com/torigiffin)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nYou can cite the seqinspector zenodo record for a specific version using the following [doi: 10.5281/zenodo.18757486](https://doi.org/10.5281/zenodo.18757486)\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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