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