I need to do custom filtration in fastq file as follows:
Remove reads having at most 2 bases under quality score 20.
Remove reads with unique sequence having read count less than 10.
I tried finding tools to do that but there is no such tool for above type of filterations. I also write some python script which use HTSeq package to read and process fastq file. But the script is extremely slow and take a day to process one file while I have 30 samples). Is there any fast way for this type of custom filtrations in fastq file.