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Start the documentation of output.md
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@ -13,6 +13,13 @@ The directories listed below will be created in the results directory after the
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The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
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- [FastQC](#fastqc) - Raw read QC
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- [falco](#falco) - Alternative to FastQC for raw read QC
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- [fastp](#fastp) - Adapter trimming for Illumina data
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- [AdapterRemoval](#adapterremoval) - Adapter trimming for Illumina data
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- [Porechop](#porechop) - Adapter removal for Oxford Nanopore data
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- [BBDuk](#bbduk) - Quality trimming and filtering for Illumina data
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- [PRINSEQ++](#prinseq++) - Quality trimming and filtering for Illunina data
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- [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
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- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
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- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
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> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
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### fastp
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fastp can automatically detect adapter sequences for Illumina data.
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<details markdown="1">
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<summary>Output files</summary>
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- `fastp`
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</details>
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### AdapterRemoval
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<details markdown="1">
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<summary>Output files</summary>
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- `adapterremoval`
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</details>
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### Porechop
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<details markdown="1">
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<summary>Output files</summary>
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- `porechop`
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- `<sample_id>.fastq.gz`
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</details>
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### BBDuk
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<details markdown="1">
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<summary>Output files</summary>
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- `bbduk`
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- `<sample_id>.bbduk.log`
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- `<sample_id>.fastq.gz`
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</details>
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### PRINSEQ++
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<details markdown="1">
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<summary>Output files</summary>
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- `prinseq++`
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</details>
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### Filtlong
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<details markdown="1">
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<summary>Output files</summary>
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- `filtlong`
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- `<sample_id>_filtered.fastq.g`
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- `<sample_id>_filtered.log`
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</details>
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### MultiQC
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<details markdown="1">
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