https://wiki.biouml.org/index.php?action=history&feed=atom&title=QUAST 2026-05-03T16:59:32Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=QUAST&diff=8400&oldid=prev 2019-03-27T12:49:21Z

<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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:49, 27 March 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The tab delimited Quast report will contain the following information::</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The tab delimited Quast report will contain the following information::</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del>Assembly&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; pit_fna cef_fna car_fna</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins>Assembly&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; pit_fna cef_fna car_fna</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del># contigs (&gt;= 0 bp)&#160; &#160; &#160; &#160; &#160; 100&#160; &#160; &#160; 91&#160; &#160; &#160; 94</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins># contigs (&gt;= 0 bp)&#160; &#160; &#160; &#160; &#160; 100&#160; &#160; &#160; 91&#160; &#160; &#160; 94</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del># contigs (&gt;= 1000 bp)&#160; &#160; &#160; &#160; 62&#160; &#160; &#160; 58&#160; &#160; &#160; 61</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins># contigs (&gt;= 1000 bp)&#160; &#160; &#160; &#160; 62&#160; &#160; &#160; 58&#160; &#160; &#160; 61</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del>Total length (&gt;= 0 bp)&#160; &#160; 6480635 6481216 6480271</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins>Total length (&gt;= 0 bp)&#160; &#160; 6480635 6481216 6480271</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del>Total length (&gt;= 1000 bp) 6466917 6468946 6467103</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins>Total length (&gt;= 1000 bp) 6466917 6468946 6467103</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del># contigs&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; 71&#160; &#160; &#160; 66&#160; &#160; &#160; 70</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins># contigs&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; 71&#160; &#160; &#160; 66&#160; &#160; &#160; 70</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> * </del>Largest contig&#160; &#160; &#160; &#160; &#160; &#160; 848753&#160; 848766&#160; 662053</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">&#160; </ins>Largest contig&#160; &#160; &#160; &#160; &#160; &#160; 848753&#160; 848766&#160; 662053</div></td></tr> </table>

Sspintus@dote.ru https://wiki.biouml.org/index.php?title=QUAST&diff=8399&oldid=prev 2019-03-27T12:48:52Z

<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;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 12:48, 27 March 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The tab delimited Quast report will contain the following information::</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The tab delimited Quast report will contain the following information::</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">&lt;nowiki&gt;</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; Assembly&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; pit_fna cef_fna car_fna</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins>Assembly&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; pit_fna cef_fna car_fna</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; # contigs (&gt;= 0 bp)&#160; &#160; &#160; &#160; &#160; 100&#160; &#160; &#160; 91&#160; &#160; &#160; 94</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins># contigs (&gt;= 0 bp)&#160; &#160; &#160; &#160; &#160; 100&#160; &#160; &#160; 91&#160; &#160; &#160; 94</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; # contigs (&gt;= 1000 bp)&#160; &#160; &#160; &#160; 62&#160; &#160; &#160; 58&#160; &#160; &#160; 61</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins># contigs (&gt;= 1000 bp)&#160; &#160; &#160; &#160; 62&#160; &#160; &#160; 58&#160; &#160; &#160; 61</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; Total length (&gt;= 0 bp)&#160; &#160; 6480635 6481216 6480271</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins>Total length (&gt;= 0 bp)&#160; &#160; 6480635 6481216 6480271</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; Total length (&gt;= 1000 bp) 6466917 6468946 6467103</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins>Total length (&gt;= 1000 bp) 6466917 6468946 6467103</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; # contigs&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; 71&#160; &#160; &#160; 66&#160; &#160; &#160; 70</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins># contigs&#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; &#160; 71&#160; &#160; &#160; 66&#160; &#160; &#160; 70</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160; Largest contig&#160; &#160; &#160; &#160; &#160; &#160; 848753&#160; 848766&#160; 662053</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160; <ins class="diffchange diffchange-inline">* </ins>Largest contig&#160; &#160; &#160; &#160; &#160; &#160; 848753&#160; 848766&#160; 662053</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">&lt;/nowiki&gt;</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> </table>

Sspintus@dote.ru https://wiki.biouml.org/index.php?title=QUAST&diff=8398&oldid=prev 2019-03-27T12:47:16Z

<p>Created page with &quot;==What it does== QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. If you have one or multiple genome assemblies, you can a...&quot;</p> <p><b>New page</b></p><div>==What it does==<br /> <br /> QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.<br /> <br /> If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page &lt;http://quast.bioinf.spbau.ru/manual.html&gt;`_.<br /> <br /> ==Using Quast without reference==<br /> <br /> Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:<br /> <br /> * Quast report in HTML format<br /> * `Contig viewer &lt;http://quast.bioinf.spbau.ru/manual.html#sec3.4&gt;`_ (an HTML file)<br /> * `Quast report &lt;http://quast.bioinf.spbau.ru/manual.html#sec3.1.1&gt;`_ in Tab-delimited format<br /> * Quast log (a file technical information about Quast tool execution)<br /> <br /> The tab delimited Quast report will contain the following information::<br /> &lt;nowiki&gt;<br /> Assembly pit_fna cef_fna car_fna<br /> # contigs (&gt;= 0 bp) 100 91 94<br /> # contigs (&gt;= 1000 bp) 62 58 61<br /> Total length (&gt;= 0 bp) 6480635 6481216 6480271<br /> Total length (&gt;= 1000 bp) 6466917 6468946 6467103<br /> # contigs 71 66 70<br /> Largest contig 848753 848766 662053<br /> &lt;/nowiki&gt;</div>

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