The pysickle from wall0159

pysickle's Introduction

Pysickle is a python implementation of sickle (https://github.com/najoshi/sickle)

NB. PLEASE NOTE THAT THIS CODE IS CURRENTLY NOT WORKING. THERE IS A BUG IN THE MOVING-AVERAGE FILTER THAT REJECTS EVERY SEQUENCE.

Pysickle takes files in the FASTQ format and uses a sliding windows and a predetermined threshold quality value to determine 5' and 3' trimming.

Pysickle takes an input fastq file and outputs a trimmed version of that file. It also has options to change the length and quality thresholds for trimming, as well as disabling 5'-trimming and enabling removal of sequences with Ns.

Pysickle currently supports three types of quality values: Illumina, Solexa, and Sanger.
	1)	"fastq" means to Sanger style FASTQ files using PHRED scores and an ASCII 
		offset of 33 (e.g. from the NCBI Short Read Archive and Illumina 1.8+).
		These can potentially hold PHRED scores from 0 to 93.

	2) "fastq-sanger" is an alias for "fastq".

	3) "fastq-solexa" means old Solexa (and also very early Illumina) style FASTQ
		files, using Solexa scores with an ASCII offset 64. These can hold Solexa
		scores from -5 to 62.

	4) "fastq-illumina" means newer Illumina 1.3 to 1.7 style FASTQ files, using
		PHRED scores but with an ASCII offset 64, allowing PHRED scores from 0
		to 62.

To run Pysickle from the working directory
$ ./pysickle.py ./test/test.fastq

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