Although it's impossible to discuss all the variations of output coming from sequencer files, paired-end reads are worth mentioning because they are common and require a different processing approach. With paired-end sequencing, both ends of a DNA fragment are sequenced with a gap in the middle (called the insert). In this case, two files will be produced: X_1.FASTQ and X_2.FASTQ. Both files will have the same order and exact same number of sequences. The first sequence will be in X_1 pairs with the first sequence of X_2, and so on. With regards to the programming technique, if you want to keep the pairing information, you might perform something like this:
f1 = gzip.open('X_1.filt.fastq.gz', 'rt, enconding='utf-8')f2 = gzip.open('X_2.filt.fastq.gz', ...
