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README.rst
fastq.cpp
fastq_pair_filter.py
guess-encoding.py
select-random-pairs.py

README.rst

fastq

summarize and filter fastq files.

build

g++ -O2 -o fastq fastq.cpp

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.

http://chart.apis.google.com/chart?chbh=a&chdl=A|C|G|T|N&chdlp=l&cht=bvs&chs=800x300&chco=FF0000,00FF00,0000FF,FFFF00,CCCCCC&chxt=x,x&chxr=0,1,76,75&chxl=1:|read%20position|&chxp=1,50&chds=0,1565&chd=t:523,548,490,474,473,461,509,462,453,509,460,455,505,507,460,455,451,452,453,503,456,501,453,451,452,453,496,498,452,498,451,451,450,448,448,448,448,494,449,448,496,447,449,494,493,447,444,443,446,446,491,447,492,446,443,445,488,446,446,446,447,447,448,488,450,444,444,444,444,444,437,443,442,444,442,439|77,20,21,27,27,75,29,28,77,28,28,32,29,30,30,29,78,76,29,31,29,29,30,76,31,31,30,31,32,31,31,78,30,32,41,32,77,31,30,78,32,31,32,31,32,32,33,81,80,34,35,35,35,82,82,41,40,39,83,44,85,47,45,45,46,50,95,98,58,57,102,63,62,106,69,70|390,496,369,316,319,325,337,375,333,337,384,381,339,340,334,387,342,340,391,344,389,346,343,343,391,392,348,346,396,348,396,351,396,396,350,349,351,352,397,349,353,400,398,355,352,354,401,354,357,403,358,402,361,356,362,406,363,364,365,366,368,409,371,371,372,414,376,377,420,383,375,381,383,385,387,425|568,499,682,745,745,701,687,697,700,688,690,694,690,686,739,692,691,695,689,685,689,687,736,693,688,685,687,686,682,683,682,679,684,683,715,729,684,682,683,683,678,682,681,679,682,725,682,680,676,676,673,673,669,674,670,662,668,709,665,703,659,655,693,653,691,652,643,640,636,674,626,671,671,624,660,624|3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,2,2,2,1,2,3,4,9,4,3,3,4,4,4,3,3,3,3,3,3,4,3,4,5,5,5,4,5,8,4,4,3,4,3,4,5,4,4,3,4,4,5,4,22,4,3,3,4,4

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.