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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

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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