ABACAS: algorithm-based automatic contiguation of assembled sequences Export

@article{citeulike:4768741, abstract = {Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk 10.1093/bioinformatics/btp347}, author = {Assefa, Samuel and Keane, Thomas M. and Otto, Thomas D. and Newbold, Chris and Berriman, Matthew}, citeulike-article-id = {4768741}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp347}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1968}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19497936}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19497936}, day = {1}, doi = {10.1093/bioinformatics/btp347}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {abacas, assembly, contig, ordering, sequencing}, month = {August}, number = {15}, pages = {1968--1969}, posted-at = {2009-10-05 16:52:16}, priority = {2}, title = {ABACAS: algorithm-based automatic contiguation of assembled sequences}, url = {http://dx.doi.org/10.1093/bioinformatics/btp347}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4768741 L3 - citeulike-article-id:4768741 N2 - Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk 10.1093/bioinformatics/btp347 IS - 15 JF - Bioinformatics SN - 1460-2059 EP - 1969 TI - ABACAS: algorithm-based automatic contiguation of assembled sequences VL - 25 SP - 1968 KW - abacas KW - assembly KW - contig KW - ordering KW - sequencing AU - Assefa, Samuel AU - Keane, Thomas AU - Otto, Thomas AU - Newbold, Chris AU - Berriman, Matthew PY - 2009/08/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp347 ER -