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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Interleaved fastq files #51

Open ValentinaPeona opened 9 months ago

ValentinaPeona commented 9 months ago

Hello,

Since I have interleaved reads ready to use, I was wondering if it is ok to use them instead of concatenating the reads or it would cause problems down the line?

Thanks!

eblerjana commented 9 months ago

Hi,

what do you mean with interleaved? In general, all reads must be in a single FASTA file.

Best, Jana

ValentinaPeona commented 9 months ago

Hi Jana,

with interleaved I mean a single fastq/fasta file in which R1 and R2 of the same pair are next to the other while a concatenated file has all the R1 reads listed and then all the R2 reads.

Best, Valentina

eblerjana commented 9 months ago

Ok I see, then that is fine. PanGenie does not use any read pair information, so any order of the reads is fine.