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