barcode_splitSplits a FASTQ/FASTA file based on sequence barcodes
 bfqConverts to/from BFQ (binary-compressed FASTQ format) (experimental)
 filterFilter out reads using a number of metrics
 mergeMerges paired FASTQ files into one file
 namesWrite out the read names
 properpairsFind properly paired reads (when fragments are filtered separately)
 revcompReverse compliment a FASTQ file
 sortSorts a FASTQ file by name or sequence
 splitSplits a FASTQ file into N chunks
 statsCalculate summary statistics for a FASTQ file
 tagAdds a prefix or suffix to the read names in a FASTQ file
 tileSplits long FASTQ reads into smaller (tiled) chunks
 trimRemove 5' and 3' linker sequences (slow, S/W aligned)
 truncateTruncates reads to a maximum length
 unmergeUnmerged paired FASTQ files into two (or more) files


 convertqualConverts qual values from Illumina to Sanger scale
 csencodeConverts color-space FASTQ file to encoded FASTQ
 fromfastaConverts (cs)FASTA/qual files to FASTQ format
 fromqseqConverts Illumina qseq (export/sorted) files to FASTQ
 tobamConverts to BAM format (unmapped)
 tofastaConverts to FASTA format (seq or qual)