Saving assembled reads as FASTQ instead of FASTA

[jflot]

Hello Nicolas,
This is a repost of a previous issue... Right now it is possible to get a FASTA of the assembled reads, but not a FASTQ. The only workaround is to get the read IDs and extract the reads from the original FASTQs, but it is rather cumbersome if I want to reassemble the reads using e.g. Unicycler (to try solve mitochondrial genome coverage issues suggesting misassemblies). Would it be possible for NOVOPlasty to export directly a the assembled reads as FASTQ instead of FASTA?
Thanks a lot in advance,
Jean-François

[ndierckx]

Hi Jean-François,

I will have a look if it easy to implement in the code, will let you know this week

[ndierckx]

Sorry for the late response, didn't had time to do it earlier, I added an extra option to save the quality scores.
I didn't took the fastest way to avoid more memory consumption, so at the end of the assembly it will just fetch it from the original files

To do this you need to put '3' for 'save assembled reads' in the config file

I will upload the new version tomorrow, need to add another update first
You can let me know if it works because have no time to test it