perfectread

Filter out erroneous reads from a collection of reads with substitution errors, keeping only perfect (error-free) reads. This project is a basic implementation of the algorithm in [].

Installation

The project require the Jellyfish software (version 2.1.4) to be already installed. The details of Jellyfish can be found at

Update the variable JELLYFISH in src/Makefile to point to the top level directory of Jellyfish 2.1.4. Compile using

$ make

Run

Update the variable JELLYFISH in src/perfectread to point to the top level directory of Jellyfish 2.1.4.

$ src/perfectread -d -t 8 -k 24 <fastq file>