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Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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James A. Fellows Yates 2023-03-03 14:58:21 +01:00 committed by GitHub
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@ -21,7 +21,7 @@ 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
- [SAMtools stats](#samtools-stats) - Statistics from host removal - [SAMtools stats](#samtools-stats) - Statistics from host removal
- [SAMtools bam2fq](#samtools-fastq) - Converts unmapped BAM file to fastq format (minimap2 only) - [SAMtools bam2fq](#samtools-bam2fq) - Converts unmapped BAM file to fastq format (minimap2 only)
- [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations - [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