Currently, GAM is composed by PERL scripts and C++ programs. The formers are used to build both frames and blocks, while the others perform conflict analysis and (super)contig weaving.

To compute blocks, use the following commands from the main directory of GAM source:
./scripts/place_reads_in_assemblies.pl <Arachne Reads File> <Aracne Link File> <PCAP Reads File> > placed.txt
./scripts/compute_assemblies_blocks.pl placed.txt 4 50 50 > blocks.txtOnce you built blocks, you can build paired(super)contigs by using the commands:
./src/build_paired_PCAP_ctgs blocks.txt <Arachne sctgs file> <Arachne fasta> <PCAP sctgs file> <PCAP fasta>
./src/build_paired_PCAP_sctgs_from_pctgs <Paired ctg fasta> <Arachne sctgs file> <Arachne fasta> <PCAP sctgs file> <PCAP fasta>Check on-line help to better understand the meaning of program parameters.

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