Fastq mcf

Introduction

fastq-mcf attempts to:

 * Detect & remove sequencing adapters and primers
 * Detect limited skewing at the ends of reads and clip
 * Detect poor quality at the ends of reads and clip
 * Detect Ns, and remove from ends
 * Remove reads with CASAVA 'Y' flag (purity filtering)
 * Discard sequences that are too short after all of the above
 * Keep multiple mate-reads in sync while doing all of the above