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README.md

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<img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
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**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (FASTQ) to provide comprehensive quality control. It 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. The 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. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
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**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It 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. The 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. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
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| `Indexing, Mapping` | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2) | Align reads to reference | [RNA, DNA] | [N/A] |
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| `Indexing` | [`SAMtools`](http://github.com/samtools) | Index aligned BAM files, create FASTA index | [DNA] | [N/A] |
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| `QC` | [`Picard`](https://broadinstitute.github.io/picard/picard-metric-definitions.html) | Collect multiple QC metrics | [RNA, DNA] | [Bwamem2, SAMtools] |
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| `Reporting` | [`MultiQC`](http://multiqc.info/) | Present QC for raw reads | [RNA, DNA, synthetic] | [N/A] |
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| `Reporting` | [`MultiQC`](http://multiqc.info/) | Aggregate and visualise results | [RNA, DNA, synthetic] | [N/A] |
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