save assembled reads in FASTQ format

[jflot]

For some very difficult, repeat-full organelle genomes I would like to get the assembled reads in FASTQ format in order to reassemble them using Unicycler. However, at present NOVOplasty only saves the assembled reads in FASTA format, and because the reads are renamed in the assembled read files I cannot even manage to extract the list of read names (which would allow me to filter the FASTQ and extract the reads used in the assembly). Would it be possible to get NOVOplasty to save assembled reads in FASTQ format?

[ndierckx]

Hi Jean-francois,

Someone else asked me before to get the original read ids, so I saw I already added an option for that. If you put "2" instead of "yes" for "Save assembled reads" in the config file, it will use the original ids. It will still not be the complete original id, but at least the unique part of it, so you can map to the original files.

Greets,

Nicolas