Currently, Novoplasty accepts only fasta and fasta.gz formats. However the tools needs to assemble small genomes from fastq.gz / fastqsanger.gz files. The input form correctly says “Select file with forward reads” and “Select file with reverse reads”. But the drop down does not allow for the selection of fastq.gz files, even when using the … (Browse or Upload Datasets option). I have in the past been able to assemble small genomes (mitochondrial genomes) with fastq.gz files using this tool before. Please help.
I am agree with you: it is a nice option to have. My point was that you still can use the tool with an additional step, FASTQ to FASTA conversion. NOVOplasty wrapper is not updated since 2021. Wrapper for an alternative tool, Get Organelle From Reads, is maintained, with the last update released in 2024, and it supports FASTQ data.
Hi @jennaj, do you know if authors of NOVOplasty wrappar plan an update with addition of FASTQ data as input?
Thanks @jrj for sharing the details and please feel free to add additional comments to the ticket above if you would like to, and if you are interested in the updated tool wrapper development yourself (or know someone interested), please do ping at the ticket and the IUC can guide you through the process.
Hope this helps!
XREF
Tutorials at the GTN (with alternative tool choices, including SPAdes/Flye)
With an organization through Assembly tutorials from a recent (now completed) training event here. → Assembly Questions can be directed to this forum as the event Slack is now closed
Tutorials at the GTN (with alternative tool choices, including SPAdes/Flye)