README for fastq_compare
Code contributed by T. Coudrat, P. Moncuquet and A. Nemri [pySickle_team3]
https://github.com/thomascoudrat/pySickle_team3
Please report bugs at adnane.nemri@csiro.au
Licence: GNU General public licence version 3
This standalone program generates a report on a single-end fastq file before and after changes were made to it, eg by a quality trimming software. For the comparison to be meaningful, the second file should be inherited from the first one. The output is stored in a file specified by the user.
Note: the program does not read fastq files of paired-end reads. \ Next update
Note: in future releases, the program is to be used alongside a quality trimming software such as Sickle
dependencies: BioPython
usage: python fastq_compare.py <BEFORE.fq> <AFTER.fq> <quality_coding> <outfile>
options for quality_coding:
phred33 Sanger and Illumina reads produced with CASAVA 1.8+
phred64 Illumina reads produced with CASAVA 1.3+
solexa Solexa reads