MinION IGS Amplicon Read Classification

Question

[j.pepin444]

Hi I'm new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi as my amplicons had ITS1 and ITS2 regions.

I have been watching Youtube tutorials on RStudio for over a week and I feel like I'm no closer than I was when I started. I have both fastq and fast5 files and I tried to run the fastq files using EPI2ME, however, the database is lacking in fungi. I have tried using NCBI's BLAST but I can only run <5kb reads and most of my sequencing reads are >6kb. Also, I've tried using Galaxy to convert my fastq files to fasta but I'm not sure how to run my long reads for species identification using Galaxy or if that is even possible.

Any help would be greatly appreciated. Thanks.

Answer 1

[colindaven]

Hi, this is an easy to use web platform:

https://bioinformatics.uni-muenster.de/tools/metag/usage/index.hbi?lang=en

Tools called centrifuge and kraken2 might help you out too (at least for first pass analyses).

In general, fungi are more neglected than bacteria and archaea in microbiome amplicon studies.