Acceptable file inputs for ShortBRED Quantify

Hello! Our lab is in the process of running ShortBRED Quantify on paired-end Illumina outputs. We have been running fastq files through ShortBRED but recently noticed that only fasta are mentioned in the tutorial. Are fastq files acceptable or should we convert to fasta?

Thank you!

FASTQ files are perfectly fine (and the norm for short reads)! We used FASTA format for the demo files because it is ~1/2 the size and the quality information lost in the FASTQ → FASTA conversion is not critical for the demo.

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