Filter fastq file (performance) about pyfastx HOT 1 OPEN

For your case, barcodes[read.id] means random access to read from file with given id. This step will firstly extract read information from index file (a sqlite database file). This may be very slow when processing large numbers of reads.

I am a little confused that why do you use read.id rather than read.name to extract reads. That means your reads in this two files are synchronous.

If you use name to extract reads from another file, you can use multiple threads to speedup.

from pyfastx.