<![CDATA[BOL: ABACAS]]> https://bioinformaticsonline.com/bookmarks/view/30973/abacas? https://bioinformaticsonline.com/bookmarks/view/30973/abacas Thu, 16 Feb 2017 12:15:55 -0600 https://bioinformaticsonline.com/bookmarks/view/30973/abacas <![CDATA[ABACAS]]> ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule. 

Address of the bookmark: http://abacas.sourceforge.net/Manual.html#9._Colour_code

]]> Surabhi Chaudhary