duk source code
March 03 2011
Mingkun Li
1. Summary
Duk is a fast, accurate,and efficent DNA sequence matching tool using Kmer hashhing method.
2. Requirement
Duk should run in any 64 bit Linux/Unix machine with g++.
3. Compile Instruction
Just type make to compile the tool.
>make
4. Manual
duk [options] ref.fa query
Options:
-o, -output <file> print log information to file, default is stdout.
-n, -nomatch <file> output the not matched reads to file,
the opton value - stands for standard output
-m, -match <file> output matched reads to file.
-k, -kmer the k mer size, default is 16.
-s, -step the step size, default is 4.
-c, -cutoff the cut off threshold for matched reads, default is 1.
-h, -help print out the help information
Identify the reads in query file whether they match to ref.fa reads.
The ref.fa must be in fasta format and the query can be in fastq or fasta format.
If there is no query file, the tool gets reads from standard input
k=16 and c=1 are recommended for small genome like bacteria or adapter removal tasks.
k=20 and c=2 are recommended for large genome such as plant.
Example:
./duk Illumina.Artifacts.fa sample.fastq
5. License
The full DUK package is distributed under FreeBSD License.
Copyright (c) 2011 <Mingkun Li>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. The name of the author may not be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
