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De Novo Assembler
EPGA2 updates some modules in EPGA which can improve memory efficiency in genome asssembly. The read library for EPGA2 should be paired-end reads. Read length shorter than 50bp 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:EPGA2). Copy all source code to this directory.
Run command line: ulimit -n 1100 //this command is used for BCALM g++ main.cpp -o EPGA -lpthread perl EPGA.pl library.txt kmerLength threadNumber Information about read libraries are stored in the file library.txt. Each line represents one read library. The first column is the first mate read file (*.fastq), the second column is the second mate read file (*.fastq), the third column is insert size of read library, the fourth column is standard deviation of insert size, the fifth column represents whether the read library is mate-paired (0 denotes paired-end reads, 1 denotes mate-paired reads). kmerLength is one integer (<32) shorter than read length which is used for building De Bruijn graph. threadNumber is thread number of program.
There are two files "contigSetLong.fa" and "scaffoldLong.fa" corresponding to final contigs and scaffolds.
Please enter the directory GAGE for evaluating results, or use QUAST to evaluate assembly results.