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