Importing files fastq.bz2 format

[llenzi (Luca)]

Hi @Danilo_Reis,

I see, I am not an ITS expert, but you may look at:

Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences

ITSxpress: a QIIME 2 plugin to trim ITS sequences Adam R. Rivers - USDA Agricultural Research Service Sveinn V. Einarsson - Dep. Microbiology and Cell Science, U. Florida & USDA Agricultural Research Service Background The internally transcribed spacer (ITS) region a widely used phylogenetic marker for fungi and other taxa. Previous work by Nilsson et al. (2009) showed that removing the conserved regions around the ITS results in more accurate taxonomic classification. An existing program, ITS…

Which it is a bit old but it may be still relevant!
To my you are good to go with starting from the raw reads,
with the possible caveat of re-orient them. For the database, I suggest to look at:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

Cheers
Luca