http://amos.sourceforge.net/wiki/index.php?action=history&feed=atom&title=UMD_Overlapper 2026-04-06T23:00:39Z Revision history for this page on the wiki MediaWiki 1.23.5 http://amos.sourceforge.net/wiki/index.php?title=UMD_Overlapper&diff=69&oldid=prev 2009-07-07T22:33:21Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 22:33, 7 July 2009</td> </tr><tr><td colspan="2" class="diff-lineno">Line 11:</td> <td colspan="2" class="diff-lineno">Line 11:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* &quot;A preprocessor for shotgun assembly of large genomes.&quot; Roberts M, Hunt BR, Yorke JA, Bolanos R, Delcher A, Journal of Computational Biology, 2004. 11(4):734-752</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* &quot;A preprocessor for shotgun assembly of large genomes.&quot; Roberts M, Hunt BR, Yorke JA, Bolanos R, Delcher A, Journal of Computational Biology, 2004. 11(4):734-752</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* &quot;Reducing storage requirements for biological sequence comparison.&quot; Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. Bioinformatics, 2004, 20(18):3363-3369.</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* &quot;Reducing storage requirements for biological sequence comparison.&quot; Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. Bioinformatics, 2004, 20(18):3363-3369.</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== More information ==</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">See: [http://www.genome.umd.edu/ http://www.genome.umd.edu/]</ins></div></td></tr> </table>

Mcschatz http://amos.sourceforge.net/wiki/index.php?title=UMD_Overlapper&diff=68&oldid=prev 2009-07-07T22:32:44Z

<p>New page: == Overview == The UMD overlapper is designed to reduce the number of overlaps produced by the assembler by reducing the number of repeat-induced overlaps. Furthermore the algorithm is gr...</p> <p><b>New page</b></p><div>== Overview ==<br /> <br /> The UMD overlapper is designed to reduce the number of overlaps produced by the assembler by reducing the number of repeat-induced overlaps. Furthermore the algorithm is greatly enhanced through the use of minimizers - a technique for reducing the number of k-mers considered in the initial phase of overlapping by an order of magnitude. Most assemblers use exact k-mer matches in order to identify reads that potentially overlap.<br /> <br /> <br /> In conjunction with the UMD overlapper, the UMD error corrector identifies and corrects potential sequencing errors by detecting bases in a multiple alignment of reads that are supported by only one of the reads. The algorithm uses a heuristic rule called the 4-3 rule that examines overlapping sets of 4 reads at 3 positions in order to <br /> identify differences corresponding to distinct copies of a repeat.<br /> <br /> <br /> == Related publications ==<br /> * &quot;A preprocessor for shotgun assembly of large genomes.&quot; Roberts M, Hunt BR, Yorke JA, Bolanos R, Delcher A, Journal of Computational Biology, 2004. 11(4):734-752<br /> * &quot;Reducing storage requirements for biological sequence comparison.&quot; Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. Bioinformatics, 2004, 20(18):3363-3369.</div>

Mcschatz