postprocessing: identify SARS-CoV-2 reads
Create FASTQ files of reads matching the SARS-CoV-2 genome.
Use bbtools
to get reads sharing kmers with the SARS-CoV-2 genome(s).
Use bbmap
instead of bbduk
: lower FP rate, higher sensitivity.
Create FASTQ files of reads matching the SARS-CoV-2 genome.
Use bbtools
to get reads sharing kmers with the SARS-CoV-2 genome(s).
Use bbmap
instead of bbduk
: lower FP rate, higher sensitivity.