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We have developed a Windows-based program, ConPath, as a scaffold analyzer which constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find out the longest acyclic graphs. Using end-read pairs of fixed-sized mate-pair library, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pairs, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including M. succiniciproducens  and V.vulinificus, where we have verified contig assembly by finding out some erroneous contigs with four kinds of error types defined in ConPath. It also supports some convenient features and viewers to investigate each contig in detail, like contig viewer, scaffold viewer, edge information list, mate-pair list, printing complex scaffolds structures, and so on.