1. How to Install EBARDenovo on Linux

mono is demanded for runing EBARDenovo on linux.

yum install gcc gcc-c++ bison pkgconfig glib2-devel gettext make libpng-devel libjpeg-devel libtiff-devel libexif-devel giflib-devel libX11-devel freetype-devel fontconfig-devel  cairo-devel httpd httpd-devel

$ wget http://download.mono-project.com/sources/libgdiplus/libgdiplus-2.10.tar.bz2
$ tar jxf libgdiplus-2.10.tar.bz2
$ ./configure --prefix=/opt/mono
$ make -j 8; make install
$ echo 'export LD_LIBRARY_PATH=/opt/mono/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
$ source ~/.bashrc

$ wget http://download.mono-project.com/sources/mono/mono-2.10.8.tar.bz2
$ tar jxf mono-2.10.8.tar.bz2
$ cd mono-2.10.8
$ ./configure --prefix=/opt/mono
$ make -j 8
$ make install
$ echo 'export PKG_CONFIG_PATH=/opt/mono/lib/pkgconfig:$PKG_CONFIG_PATH' >> ~/.bashrc
$ echo 'export PATH=/opt/mono/bin:$PATH' >> ~/.bashrc
$ source ~/.bashrc

$ wget http://ncu.dl.sourceforge.net/project/ebardenovo/EBARDenovo-1.2.2-20130404.zip
$ unzip EBARDenovo-1.2.2-20130404.zip
$ cd EBARDenovo-1.2.2-20130404/
$ mono EBARDenovo.exe -h

2. The parameters

Display parameters
-l :  no log file
-v :  no verbose mode

Quality parameters
-k (default 15): key size
-c (default 0) : minimal size of contig
-n (default 10): nail size
-e (default 8) : errors per N bp

Optional output parameters
-A : Ouput analysis information including coverage and alignment.
-G : skip output information for contig/gene groups to xxx-groups.txt
-P : skip output SNPs of contigs to xxx-snps.txt
-O : output small overlaps (<24bp) inside contigs to xxx-overlaps.fa
-L : output chimeric segments to xxx-delutions.fa

Execution parameters
-a : action 1: only building index files; action 2: save indices before assembly; action 3: action is to do assembly directly.
-d : the directory of index files.
-T : running threads of accelerating assembly

Help
-h

3. Several examples of running EBARDenovo

1. Most simplest
$ mono EBARDenovo.exe [-T 24] -o contigs.fasta read1.fq.gz read2.fq.gz

2. Using two stages of indexing and assembly (used usually):
$ mono EBARDenovo.exe -a 1 -d index -T 24 \
-c 200 -o contigs.fasta read1.fq.gz read2.fq.gz
$ mono EBARDenovo.exe -a 3 -d index -T 24 \
-c 200 -o contigs.fasta read1.fq.gz read2.fq.gz

3. With full calculation and parameters
$ mono EBARDenovo.exe -A -a 2 -d index -T 24 \
-k 15 -c 200 -n 10 -e 8 -O -L \
-o contigs.fasta read1.fq.gz read2.fq.gz

4. 注意事项

使用该软件应用于转录组的De novo组装，貌似要求short reads的长度要一致。
当使用的reads数据量过大的时候，容易出错：

Build indx (Bulks of 100000 spots) ...1 2 3 4 5 6 7 8 9 10 11 12 Too many heap sections: Increase MAXHINCR or MAX_HEAP_SECTS
Stacktrace:

  at (wrapper managed-to-native) object.__icall_wrapper_mono_array_new_specific (intptr,int) <0xffffffff>
  at BioAsia.GSLib.TxtNgsReader.RechargeBuf () <0x0003b>
  at BioAsia.GSLib.TxtNgsReader.Peek () <0x000eb>
  at BioAsia.GSLib.FastqNgsReader.ReadSeqLine () <0x00083>
  at BioAsia.EbarDenovo.EbarIndexing.BuildIndicesAndPairs (System.Collections.Generic.List`1) <0x007ea>
  at BioAsia.EbarDenovo.EbarIndexing.Build () <0x00283>
  at BioAsia.EbarDenovo.Program.Main (string[]) <0x0021b>
  at (wrapper runtime-invoke) .runtime_invoke_void_object (object,intptr,intptr,intptr) <0xffffffff>

Native stacktrace:

        mono() [0x495e64]
        /lib64/libpthread.so.0(+0xf500) [0x7fd088d7a500]
        /lib64/libc.so.6(gsignal+0x35) [0x7fd088a0a8e5]
        /lib64/libc.so.6(abort+0x175) [0x7fd088a0c0c5]
        mono() [0x5e8375]
        mono() [0x5e0108]
        mono() [0x5e058d]