KrakenUniq read extraction

[SannaAb]

KrakenUniq read extraction

[jfy133]

And we will do a 1.1.7 patch release with a couple of other bug fixes very soon :)

[jfy133]

Hi @SannaAb ,

Huh ok interesting. Can you confirm: are your input reads for both Illumina and iontorrent FASTQ or FASTA?

I'm wonderinf KrakenUniq just spits out reads in the same format as the input? In which case, yeah we made a false assumption in the module thinking the output is always FASTA but maybe it is not.

[jfy133]

OK I think we've found the case:

KrakenUniq automatically can read internally either FASTA or FASTQ, but it forces you to 'name' the entire output file yourself (including extension). I think we made a faulty assumption(? - @Midnighter ) it's always FASTA, whereas it'll actually just spit out the same format as was given as input.

We will need to update the module to 'auto-detect' the input format, and save the classified reads with the same suffix.

[Midnighter]

I see now the relation to your other comment. sigh