Large Scale Genome assembler
Installation
dependencies:
- [GCC version 4.1 or larger] (http://gcc.gnu.org)
- [MPICH version 1.4 or larger] (http://www.mpich.org) compile and install： make
Parameters
- 'k': size of k-mer (bp), odd number less than 127. ['23']
- 'c': cutoff threshold for edges and k-melecules. ['0']
- 'i': the dataset file in fasta format.
- 'o': the directory for all the output files.
- 'h': help information for the usage of SWAP-Assembler.
- 'v': version information of SWAP-Assembler.
- 's': output the kmer Graph in file kmerGraph.txt.
- 'j': output the Jung Graph in file JungGraph_arc.txt and JungGraph_mul.txt.
- 'd': output the contig graph in file contigGraph.txt.
Example
mpirun -np 24 ./Largo -k 63 -c 5 -i ./data/S.aureus.fasta -o Saur_k31_c5