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Update output.md
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@ -23,10 +23,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
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- [Bowtie2](#bowtie2) - Host removal for Illumina reads
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- [minimap2](#minimap2) - Host removal for Nanopore reads
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- [samtoolsstats](#samtoolsstats) - Statistics from host removal
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- [cat] - **WIP**
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- [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
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- [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
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- [Bracken](#bracken) -
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- [Centrifuge](#centrifuge) - Taxonomic classifier that uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
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- [Kaiju](#kaiju) - Taxonomic classifier that finds maximum (in-)exact matches on the protein-level.
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- [Diamond](#diamond) - Sequence aligner for protein and translated DNA searches.
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- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
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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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@ -145,15 +148,6 @@ fastp can automatically detect adapter sequences for Illumina data.
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</details>
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### cat
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<details markdown="1">
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<summary>Output files</summary>
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- `cat`
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</details>
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### Kraken2
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<details markdown="1">
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@ -182,9 +176,51 @@ fastp can automatically detect adapter sequences for Illumina data.
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</details>
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### Centrifuge
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<details markdown="1">
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<summary>Output files</summary>
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- `centrifuge`
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- `<sample_id>.centrifuge.mapped.fastq.gz`
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- `<sample_id>.centrifuge.report.txt`
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- `<sample_id>.centrifuge.results.txt`
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- `<sample_id>.centrifuge.unmapped.fastq.gz`
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</details>
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### Kaiju
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<details markdown="1">
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<summary>Output files</summary>
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- `kaiju`
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- `<sample_id>.tsv`
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</details>
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### Diamond
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<details markdown="1">
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<summary>Output files</summary>
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- `diamond`
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- `<sample_id>.log`
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- `<sample_id>.sam`
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</details>
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### mOTUs
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<details markdown="1">
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<summary>Output files</summary>
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- `motus`
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- `<sample_id>.log`
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- `<sample_id>.out`
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</details>
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=======
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>>>>>>> 6d0b5d0a58d92fabfc239818f272bb06cfeb1e66
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### MultiQC
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<details markdown="1">
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