PAGIT is a tool to improve the quality of genomes that have already been assembled. It performs subsequent steps needed from the point of contig assembly, which includes closing gaps, error correction of consensus sequence and use other closely related reference genomes to scaffold and generate annotation. PAGIT bundles the software ABACAS, IMAGE, iCORN and RATT.
Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD "A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs." Nat Protoc. 2012 Jun 7;7(7):1260-84. https://doi.org/10.1038/nprot.2012.068
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