NAME

       sak - Slicing and dicing of FASTA/FASTQ files..

       SYNOPSIS

              sak [OPTIONS] [\B-o OUT.{fa,fq}] IN.{fa,fq}

       DESCRIPTION

              "It slices, it dices and it makes the laundry!"

              Rewrite of the original SAK tool by Manuel Holtgrewe.

       -h, --help

              Displays this help message.

       --version

              Display version information

              Output Options:

       -o, --out-path FASTX

              Path  to  the  resulting  file. If omitted, result is printed to stdout.  Use files
              ending in .fq or . to write out FASTQ.  Valid  filetypes  are:  .fq,  .fastq,  .fa,
              .fasta, .faa, .ffn, .fna, and .frn.

       -rc, --revcomp

              Reverse-complement output.

       -l, --max-length LEN

              Maximal number of sequence characters to write out.

              Filter Options:

       -s, --sequence NUM

              Select the given sequence for extraction by 0-based index.

       -sn, --sequence-name NAME

              Select sequence with name prefix being NAME.

       -ss, --sequences RANGE

              Select sequences from-to where from and to are 0-based indices.

       -i, --infix RANGE

              Select characters from-to where from and to are 0-based indices.

       -ll, --line-length LEN

              Set  line  length  in  output  file. See section Line Length for details.  In range
              [-1..inf].

       LINE LENGTH

              You can use the setting --line-length for setting the  resulting  line  length.  By
              default,  sequences  in FASTA files are written with at most 70 characters per line
              and sequences in FASTQ files are written  without  any  line  breaks.  The  quality
              sequence in FASTQ file is written in the same way as the residue sequence.

              The  default  is  selected  with a --line-length value of -1 and line breaks can be
              disabled with a value of 0.

       USAGE EXAMPLES

              sak -s 10 IN.fa

              Cut out 11th sequence from IN.fa and write to stdout as FASTA.

              sak -ss 10-12 -ss 100-200 IN.fq

              Cut out 11th up to and including 12th and 101th up to and including 199th  sequence
              from IN.fq and write to stdout as FASTA.

       VERSION

              sak version: 0.2 Last update November 2012