Kraken2 on forward reads

Question

[pramach1]

Can kraken2 analysis be done only on forward reads. If yes, what could be the option for --paired?

kraken2 --use-names -db /lustre/db/kraken/minikraken2_v1_8GB --paired /Common/44R2_L001_R1_001.fastq.gz /Common/44R2_L001_R2_001.fastq.gz --output /kb_out/krakNbrackn_output/kraken_results_44R2.txt --report /kb_out/krakNbrackn_output/44R2.txt

Answer 1

[GenoMax]

--paired by definition can't be for one read file.

To get a full list of options, use kraken2 --help

[Istvan Albert]

just to expand on this since the answer by GenoMax may sound too condensed

don't run your tool in paired-end mode if you only want to run a single read, treat that file as if it were single-end,