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bioinfo-ut / StrainSeeker

A bacterial identification program for fast identification of bacterial strains from raw sequencing reads
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StrainSeeker with paired end reads #6

Open termithorbor opened 3 years ago

termithorbor commented 3 years ago

Hi,

how do I analyse paired end Illumina sequencing data with StrainSeeker. Do I need to concatenate the forward and reverse reads in a single file or should the search seperately performed on the forward and reverse reads?

Thanks in advance :)

mihkelvaher commented 3 years ago

Hi!

Since all sequencing data is analysed as a whole the files should be concatenated.

termithorbor commented 3 years ago

Thanks :)

termithorbor commented 3 years ago

Hi, and do I need to quality filter the reads before? If so, which software would you recommend? Thanks in advance :)

mihkelvaher commented 3 years ago

Hi! The effect of quality filtering depends on the database but it's usually a good idea regardless. I've been using fastp myself.