fastqutils

General
	barcode_split	Splits a FASTQ/FASTA file based on sequence barcodes
	bfq	Converts to/from BFQ (binary-compressed FASTQ format) (experimental)
	filter	Filter out reads using a number of metrics
	merge	Merges paired FASTQ files into one file
	names	Write out the read names
	properpairs	Find properly paired reads (when fragments are filtered separately)
	revcomp	Reverse compliment a FASTQ file
	sort	Sorts a FASTQ file by name or sequence
	split	Splits a FASTQ file into N chunks
	stats	Calculate summary statistics for a FASTQ file
	tag	Adds a prefix or suffix to the read names in a FASTQ file
	tile	Splits long FASTQ reads into smaller (tiled) chunks
	trim	Remove 5' and 3' linker sequences (slow, S/W aligned)
	truncate	Truncates reads to a maximum length
	unmerge	Unmerged paired FASTQ files into two (or more) files
Conversion
	convertqual	Converts qual values from Illumina to Sanger scale
	csencode	Converts color-space FASTQ file to encoded FASTQ
	fromfasta	Converts (cs)FASTA/qual files to FASTQ format
	fromqseq	Converts Illumina qseq (export/sorted) files to FASTQ
	tobam	Converts to BAM format (unmapped)
	tofasta	Converts to FASTA format (seq or qual)