This program generates a genome graph
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To compile the program: i. Go to the src directory ii.make
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Change the library path to the 'src' directory export LD_LIBRARY_PATH= [...]/src
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Input Fasta file should be changed to the foramt is acceptable by the program run: ../src/graph fasta_prepare prepared_fasta input1_fasta input2_fasta [...] inputn_fasta
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Use the prepared_fasta to generate a maf file contains pairwise alignments Any aligner can be used
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After having the input_maf file, to built the graph run: ../src/graph build_graph prepared_fasta input_maf output_maf output_encode(noencode) output_fasta ourput_dot output_gfa(nogfa) output_txt 0(1) number_of_threads(optional)
0: generate graphs with longer nodes 1: generate graphs with shorter nodes noencode: if don't need the arithmetically encoded output file nogfa: if dont' need the gfa output file
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To decode the output_encode ../src/graph dy_decoding output_encode 0(1) output_decode
0 or 1 determine the center type which was used in buildign the graph.