Taxonomic identification of NGS reads

Question

[Lora]

Hello everyone,
do you maybe know if there is a tool available for taxonomic identification of NGS reads (Linux)? Meaning that short paired-end reads would be used as an input, to get a blast-like information on taxonomy of the sequenced samples as an output. Thank you.

[Sej Modha]

There are plenty of options...see this paper for further details and pick a tool that suits your requirements: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6716367/

Answer 1

[Sean Davis]

I'm not sure in what context you want to do this, but fastq-screen can be useful for overall summaries. However, if you are instead talking about metagenomic or microbiome analysis, you'll probably want to look into tools that are specifically designed for quantification in that context such as BioBakery.

[Lora]

Hi Sean,
thank you for your reply. my purpose is to detect field misidentifications among my 160 samples (tree species). I will try fastq-screen, but I don't know if it's connected to a sort of database (such as NCBI's GenBank)?
All best

Answer 2

[GenoMax]

You can try STAT: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02490-0

NCBI uses this tool to create the taxonomic representation of SRA records.