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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Sofia Stamouli 2023-01-11 16:46:30 +01:00 committed by GitHub
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@ -29,6 +29,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [Centrifuge](#centrifuge) - Taxonomic classifier that uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. - [Centrifuge](#centrifuge) - Taxonomic classifier that uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
- [Kaiju](#kaiju) - Taxonomic classifier that finds maximum (in-)exact matches on the protein-level. - [Kaiju](#kaiju) - Taxonomic classifier that finds maximum (in-)exact matches on the protein-level.
- [Diamond](#diamond) - Sequence aligner for protein and translated DNA searches. - [Diamond](#diamond) - Sequence aligner for protein and translated DNA searches.
- [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics
- [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling. - [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution