I want to use Kraken2 for filtering reads. Because of the number of sample I process, I can not keep the reads uncompressed. I know you can "trick" the program by redirecting the output to stdout but this solution does not work for paired data. Is there any chance an output compression option is implemented ? Or any kind of option that allow to bgzip the output directly, such as interleaved fastq ?
Thank you
Hello,
I want to use Kraken2 for filtering reads. Because of the number of sample I process, I can not keep the reads uncompressed. I know you can "trick" the program by redirecting the output to stdout but this solution does not work for paired data. Is there any chance an output compression option is implemented ? Or any kind of option that allow to bgzip the output directly, such as interleaved fastq ? Thank you