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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Sofia Stamouli 2022-12-20 17:33:35 +01:00 committed by GitHub
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@ -23,6 +23,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [Bowtie2](#bowtie2) - Host removal for Illumina reads - [Bowtie2](#bowtie2) - Host removal for Illumina reads
- [minimap2](#minimap2) - Host removal for Nanopore reads - [minimap2](#minimap2) - Host removal for Nanopore reads
- [samtoolsstats](#samtoolsstats) - Statistics from host removal - [samtoolsstats](#samtoolsstats) - Statistics from host removal
- [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations
- [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches - [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
- [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species - [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
- [Bracken](#bracken) - - [Bracken](#bracken) -