fastq

summarize and filter fastq files.

build

g++ -O2 -o fastq fastq.c

usage

summarize

codon usage table:

fastq summarize --adjust 64 --codon some.fastq

creates a table (to STDOUT) and a link to a google api chart showing codon usage at each basepair in the read.

quality usage table:

fastq summarize --adjust 64 --codon some.fastq

creates a table with columns of quality values for percentiles: 0.01, 0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95, 0.99 and for median. each row is a read position (useful for seeing how quality declines with increasing read position).

filter

run ./fastq with no arguments to see help for filtering.