How to filter low quality Kmers in raw fastq file

[yhg926]

Hi, Dr Zhao: Does bindash have option to filter out low coverage or low quality Kmers in fastq file? I believe these Kmers will bias distance estimation Many thanks

[zhaoxiaofei]

Sorry for the extremely late reply. BinDash has no option to filter out low coverage or low quality k-mers in fastq files. I believe that, in theory, these low-quality k-mers would add no bias to the distance estimation, but it would add variance to the bias estimation, causing more random noise. Please feel free to open a feature request for discarding k-mer with any low base quality if you would like.