Taxanomic classification of unpaired reads in paired-end read files with Kraken2 with --paired flag
I am classifying metagenomic paired end reads using Kraken2's --paired flag. I was wondering, if after quality control there are unpaired reads in either file, will Kraken2 classify the unpaired read without any errors? Is it advisable to carryout classification with unpaired reads?
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How did you end up with unpaired reads? Generally scan/trim programs will remove both reads when one of them fails set limits. You are not supposed to scan/trim paired-end data files independently since doing that throws the reads out-of-sync in the two files.
I am using kneaddata. It uses trimmomatic to carry out trimming which generates separate output files for reads that has no mate (unpaired reads).