Provided by: seqan-apps_1.4.1+dfsg-2_amd64 
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