rhinogradentia/fastq_corrupt_check

Check a FASTQ file to see if it is corrupt

fastq_corrupt_check

Check a FASTQ file to see if it is corrupt

Usage:

fastq_corrupt_check can accept any number of fastq files, and will check all files mentioned after perl fastq_corrupt_check.pl

perl fastq_corrupt_check.pl file1 file2

where each file has fastq or fq at the end, with no compression, gz compression, or bz2 compression.

perl fastq_corrupt_check.pl file.fastq.bz2 file0.fq.gz file1.fastq

How it Works

This short program was inspired by FastQC, which did not check for file corruption. fastq_corrupt_check.pl checks to ensure that Fastq files are not corrupted. Each entry in a Fastq file has 4 lines. The fastq file should have the following properties:

* The 2nd line should only consist of A, C, G, T, and/or N
* The length of the 4th line matches the length of the 2nd line
* The 3rd line must start with a '+'
* The file should have an integral multiple of 4 number of lines.

This program is not complicated. It is meant as a timesaver. I am putting it here because FastQC didn't noticed that a file was corrupted in transfer.