Closed kapsakcj closed 3 years ago
This behavior is desinged intentionally. There is a sub-sampling process in the workflow of k-mer raw reads mode. Instead of using all the input raw reads, SeqSero2 only uses sub-sampled reads in the k-mer raw reads workflow for rapid serotype prediction, and normally only forward reads are used for the analysis. Listing the first pair of reads as input files is to indicate that not all reads were used in the analysis.
Thanks for the explanation, I was unaware that it did that!
When I run SeqSero2 v1.0.0 using
-m k -t 2 -i R1.fastq.gz R2.fastq.gz
options, the output only lists the first of my pair of reads for an isolate. Allele mode-m a
does not show this behavior, and lists both input files in the output.