Eight PERL scripts.
remap_qualifiedASM.pl
strict_filter.pl - Refine the MUMmer alignment
aln_extract.pl - Extract sequence from MUMmer alignment
core_genome_build.pl - Build (relaxed) core genome based on sequences in MUMmer alignment
core_remove_region.pl - Remove repetitive regions or other regions
core_map2snp.pl - Extract SNPs from the core genome
nucmer_filter.pl - A integrated script that run MUMmer to generate a mapped sequence
core_snp2fas.pl - Build a SNP-only alignment based on SNPs extracted.

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2014-04-25
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