TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
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Add preliminary step: Host Removal via Alignment #33
Instead of only giving the option to use Kraken2 for de-hosting, provide minimap2/bowtie2 and save unaligned reads to another fastq file (.gz)
Additional parameters to add:
Reference for Host FASTA file (single file)
List of Taxid's (separated by space, integer value) to pull from NCBI (use assembly refseq file for mapping taxid to genome(s)).
Disable/Enable Stats that includes metrics on the host read removals. Add multiqc area with sufficient headers to mention these stats and differentiate from the downstream alignment steps post-kraken2
Merritt-Brian
commented
10 months ago
Description of feature
Instead of only giving the option to use Kraken2 for de-hosting, provide minimap2/bowtie2 and save unaligned reads to another fastq file (.gz)
Additional parameters to add: