fastq2table.py - compute stats on reads in fastq files

Tags

Genomics NGS Sequences FASTQ Annotation

Purpose

This script iterates over a fastq file and outputs summary statistics for each read.

The output is a tab-delimited text file with the following columns:

Column	Content
read	read identifier present in input fastq file
nfailed	number of reads that fall below Q10
nN	number of ambiguous base calls (N)
nval	number of bases in the read
min	minimum base quality score for the read
max	maximum base quality for the read
mean	mean base quality for the read
median	median base quality for the read
stddev	standard devitation of quality scores for the read
sum	sum of quality scores for the read
q1	25th percentile of quality scores for the read
q3	25th percentile of quality scores for the read

Usage

Example:

cgat fastq2table --guess-format=sanger < in.fastq > out.tsv

In this example we know that our data have quality scores formatted as sanger. Given that illumina-1.8 quality scores are highly overlapping with sanger, this option defaults to sanger qualities. In default mode the script may not be able to distinguish highly overlapping sets of quality scores.

If we provide two reads to the script:

@DHKW5DQ1:308:D28FGACXX:5:2211:8051:4398
ACAATGTCCTGATGTGAATGCCCCTACTATTCAGATCGCTTAGGGCATGC
+
B1=?DFDDHHFFHIJJIJGGIJGFIEE9CHIIFEGGIIJGIGIGIIDGHI
@DHKW5DQ1:308:D28FGACXX:5:1315:15039:83265
GAATGCCCCTACTATTCAGATCGCTTAGGGCATGCGTCGCATGTGAGTAA
+
@@@FDFFFHGHHHJIIIJIGHIJJIGHGHC9FBFBGHIIEGHIGC>F@FA

we get the following table as output:

read	nfailed	nN	nval	min	max	mean	median	stddev	sum	q1	q3
DHKW5DQ1:308:D28FGACXX:5:2211:8051:4398	0	0	50	16.0000	41.0000	37.2000	38.0000	4.4900	1860.0000	36.0000	40.0000
DHKW5DQ1:308:D28FGACXX:5:1315:15039:83265	0	0	50	24.0000	41.0000	37.0200	38.0000	3.5916	1851.0000	36.0000	40.0000

Type:

cgat fastq2table --help

for command line help.

Command line options

usage: fastq2table [-h] [--version]
                   [--guess-format {sanger,solexa,phred64,illumina-1.8,integer}]
                   [--target-format {sanger,solexa,phred64,illumina-1.8,integer}]
                   [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
                   [--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                   [--log-config-filename LOG_CONFIG_FILENAME]
                   [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                   [-E STDERR] [-S STDOUT]
fastq2table: error: argument -?: expected one argument