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.
Changes were made to the download_fastas.py script:
Implementation of a "retry" loop that attempts to redownload NCBI RefSeq genomes three times in case of failure
Standardization of downloaded assembly for corresponding taxids. For taxa that have complete genomes but are not reference genomes, code has been modified to ensure that a consistent reference_id is retrieved.
Changes were made to the download_fastas.py script: