De Novo Assembler
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GAGE
README.md
bitarray.h
common.h
constructcontigset.h
contigmerge.h
dfs.h
fillgap.h
graph.h
kmerset.h
main.cpp
readset.h
scaffolding.h

README.md

License

Copyright (C) 2014 Jianxin Wang(jxwang@mail.csu.edu.cn),Junwei Luo(luojunwei@csu.edu.cn)

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses/.

Jianxin Wang(jxwang@mail.csu.edu.cn),Junwei Luo(luojunwei@csu.edu.cn) School of Information Science and Engineering Central South University ChangSha CHINA, 410083

De Novo Assembler

EPGA is used for paired-read libraries of read length shorter than 40bp and coverage larger than 100.

1)Installing.

EPGA is written C++ and therefore will require a machine with GNU C++ pre-installed.

Create a main directory (eg:EPGA). Copy all source code to this directory.

Run command line: g++ main.cpp -o epga -lpthread

2)Running.

./epga libraryName insertsize sd libraryName1 insertsize1 sd1 kmerLength threadNumber

libraryName is paired-end reads file name in Fasta format (eg: read1.fa). Paired-end reads are in single file. Left mate read and right mate read stored in file one by one.(For mate-paired reads, please transform them to paired-end reads.)

insertsize is the sequence fragment length about paired-end reads (eg: 500).

sd is the standard deviation of insertsize.

kmerLength is one integer shorter than read length which is used for building De Bruijn graph.

threadNumber is thread number of program.

3)Evaluation. Please enter the directory GAGE for evaluate assembly results, or use QUAST to evaluate assembly results.