msettles
commented
4 years ago partial solution implemented #183 with 'bases my cycle' and 'quality by cycle' matrices for each read added to the json output.
Last thing I'd like to add before closing is something for "over-represented sequences" Idea is store all kmers found in the first N sequences, then count their occurrence in the whole dataset, print out anything that reaches a certain threshold of occurrence, say 0.1%. Parameters might be
-k [ --kmer ] arg (=36)
-r [ --kmer-offset ] arg (=1)
-n [--number_of_reads] arg(=500000) number of reads to establish kmer set
-o [--occurence] arg(=0.001) The occurence of a kmer to output
Not sure everything that should be in here - but a place hold for this feature request.