Advertise with Googlier.com https://bioinf.spbau.ru en https://bioinf.spbau.ru/en/content/spades-311-released <p>A new version of SPAdes if finally out. In this release you will see many nice improvements, such as</p> <ul> <li>Reworked IonHammer module</li> <li>Major improvements in metaSPAdes pipeline</li> <li>Support for strand-specific data and coverage-based isoform detection in rnaSPAdes</li> <li>exSPAnder repeat resolution is improved in terms of both performance&nbsp;and repeat resolution accuracy</li> <li>Better RAM consumption and running time in general</li> <li>Improved careful mode for isolate datasets&nbsp;</li> <li>Several important bug-fixes</li> </ul> News Public Mon, 04 Sep 2017 08:40:07 +0000 andrey 511 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/spades_3_9 <p>&nbsp;</p> <p class="p1"><span class="s1">We are happy to announce that we have just released new <a href="http://bioinf.spbau.ru/en/spades">SPAdes 3.9.0</a>. In this version, we have included rnaSPAdes – a de novo transcriptome assembler for RNA-Seq data.</span></p> Public Sat, 23 Jul 2016 18:09:18 +0000 vlad 509 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/spades_3_8 <p>&nbsp;</p> <p>&nbsp;</p> <p><header class="entry-header" style="box-sizing: border-box; color: rgb(17, 13, 9); font-family: Roboto, sans-serif; font-size: 18px; letter-spacing: 0.5px; line-height: 29.16px;"><br /> <h1 class="entry-title" style="box-sizing: border-box; font-size: 22px; margin: 0px 0px 25px; font-family: 'Open Sans', sans-serif; line-height: 1.1; color: rgb(43, 60, 77); letter-spacing: 1px; text-transform: uppercase;">&nbsp;</h1> <p></p></header> </p> <p>&nbsp;</p> <p>&nbsp;</p> <div class="entry-content" style="box-sizing: border-box; color: rgb(17, 13, 9); font-family: Roboto, sans-serif; font-size: 18px; letter-spacing: 0.5px; line-height: 29.16px;"> <p style="box-sizing: border-box; margin: 0px 0px 10px;">We have just released a new version of SPAdes, which includes the following features and modifications:</p> <ul style="box-sizing: border-box; margin-bottom: 10px;"> <li id="" style="box-sizing: border-box;">plasmidSPAdes&nbsp;– a pipeline for extracting and assembling plasmids from WGS data;</li> <li style="box-sizing: border-box;">major improvements in metaSPAdes;</li> <li style="box-sizing: border-box;">several performance improvements.</li> </ul> <p style="box-sizing: border-box; margin: 0px 0px 10px;"><a href="http://cab.spbu.ru/software/spades/" style="box-sizing: border-box; color: rgb(193, 87, 40); background: transparent;">Try SPAdes 3.8&nbsp;now!</a></p> </div> <p>&nbsp;</p> <p>&nbsp;</p> Public Tue, 31 May 2016 14:09:31 +0000 vlad 508 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/spades3.7 <p id="aeaoofnhgocdbnbeljkmbjdmhbcokfdb-mousedown" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;">We are happy to announce that we have just released new&nbsp;SPAdes 3.7.0<span style="font-size: 12.8px;">. This version includes metaSPAdes metagenomic pipeline and many other improvements and fixes.</span></p> <p style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;">Please note that SPAdes is not intended for large genomes (e.g. mammalian size genomes). Should you decide to use SPAdes for a larger genome, please be aware that you are doing it at your own risk.</p> <p style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;">SPAdes version 3.7.0 is released under GPLv2 and openly available for download from&nbsp;<a href="http://bioinf.spbau.ru/en/spades" style="color: rgb(17, 85, 204);" target="_blank">http://bioinf.spbau.ru/en/<wbr>spades</wbr></a>.</p> <p><wbr></wbr></p> <p><wbr></wbr></p> <p><wbr> <p><wbr></wbr></p> <p><wbr><wbr> <p><wbr></wbr></p> <p><wbr><wbr> <p><wbr></wbr></p> <p><wbr><wbr><wbr><br /> <p style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;">Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please provide us with the files&nbsp;<b>params.txt</b>&nbsp;and&nbsp;<b>spades.log</b>&nbsp;from the output directory. Address for communications:&nbsp;<a href="mailto:spades.support@bioinf.spbau.ru" style="color: rgb(17, 85, 204);" target="_blank">spades.support@bioinf.spbau.ru</a><wbr>.</wbr></p> <p><wbr><wbr> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> </wbr></wbr></p> </wbr></wbr></wbr></p></wbr></wbr></p></wbr></wbr></p></wbr></p> Public Wed, 24 Feb 2016 16:58:16 +0000 vlad 505 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/content/rnaquast-released <p><span style="font-family: Slack-Lato, appleLogo, sans-serif; font-size: 15px; line-height: 22px;">rnaQUAST is a tool for evaluating quality of transcriptome assemblies using reference genome and gene database. You can download <a href="http://bioinf.spbau.ru/ru/rnaquast">here the first stable release</a>.&nbsp;</span></p> Public Wed, 13 Jan 2016 18:52:32 +0000 vlad 504 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/spades_3_6_2 <div id="fb-root" style="color: rgb(68, 68, 68); font-family: 'Trebuchet MS', 'Helvetica neue', Helvetica, Arial, Verdana, sans-serif; font-size: 13px; line-height: 19.5px;">A bug-fix release SPAdes 3.6.2 is available. Please consider updating SPAdes:&nbsp;<a href="http://bioinf.spbau.ru/en/spades">http://bioinf.spbau.ru/en/spades</a></div> <div id="fb-root" style="color: rgb(68, 68, 68); font-family: 'Trebuchet MS', 'Helvetica neue', Helvetica, Arial, Verdana, sans-serif; font-size: 13px; line-height: 19.5px;"> <p>&nbsp;</p> </div> Public Thu, 19 Nov 2015 13:54:11 +0000 vlad 503 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/content/spades-361-available-bug-fix-release <div id="fb-root" style="color: rgb(68, 68, 68); font-family: 'Trebuchet MS', 'Helvetica neue', Helvetica, Arial, Verdana, sans-serif; font-size: 13px; line-height: 19.5px;"><span style="font-size: 72px;"><strong style="font-size: 24px;">SPAdes 3.6.1 is available!</strong></span><strong style="font-size: 24px;">&nbsp;</strong></div> <div id="fb-root" style="color: rgb(68, 68, 68); font-family: 'Trebuchet MS', 'Helvetica neue', Helvetica, Arial, Verdana, sans-serif; font-size: 13px; line-height: 19.5px;"> <p><em><strong><span style="font-size: 16px;">A bug-fix release.&nbsp;</span></strong></em></p> <p>Please consider updating SPAdes:&nbsp;<a href="http://bioinf.spbau.ru/en/spades">http://bioinf.spbau.ru/en/spades</a></p> </div> Public Wed, 07 Oct 2015 10:16:56 +0000 vlad 501 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/metaquast-3-1-released <p>QUAST 3.1 released! Even better, faster, and much lighter than QUAST 3.0.</p> <ul> <li>Significantly reduced size of the installation package</li> <li><a href="http://bioinf.spbau.ru/en/metaquast">MetaQUAST</a> includes Krona charts, heatmaps, and many other new features</li> </ul> <div><a href="http://quast.bioinf.spbau.ru/metaquast/metahit/summary/report.html"><img alt="http://quast.bioinf.spbau.ru/metaquast/metahit/summary/report.html" src="http://bioinf.spbau.ru/sites/default/files/metahit_smaller_screenshot.png" style="width: 100%; height: 100%;" /></a></div> <div> <p style="text-align: center;"><a href="https://sourceforge.net/projects/quast/files/"><button><span style="font-size: 24px;"><strong>Download</strong></span></button></a></p> <div style="height: 10px;"> <div style="height: 10px;">&nbsp;</div> </div> </div> <style type="text/css"> ul.mylist { margin-bottom: 1em; } ul.mylist li:first-child { margin-top: -0.7em; } ul.mylist li { margin-left: 10px; }</style> Public Tue, 25 Aug 2015 16:31:08 +0000 vlad 500 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/content/spades-36-better-performance-truspades-truseq-long-reads <p style="font-size: medium;"><a href="http://bioinf.spbau.ru/spades">SPAdes 3.6</a> is out!</p> <p style="font-size: medium;">NEW: Added truSPAdes – an assembler for short reads produced by Illumina TruSeq Long Read technology.</p> <p style="font-size: medium;">Changes:</p> <ul> <li style="font-size: medium;">Better running time, less RAM consumption and improved results for BayesHammer error correction module.</li> <li style="font-size: medium;">Improvements and bugfixes in repeat resolution and scaffolding modules.</li> <li style="font-size: medium;">Improvements and bugfixes in dipSPAdes.</li> <li style="font-size: medium;">MismatchCorrector now uses bwa-mem.</li> <li style="font-size: medium;">Bugfixes in MismatchCorrector.</li> </ul> Public Tue, 18 Aug 2015 12:55:42 +0000 vlad 499 at https://bioinf.spbau.ru https://bioinf.spbau.ru/en/content/quast-3-out <p>Brand new version of QUAST is released!</p> <ul> <li><strong>Faster:&nbsp;</strong>5x–100x more running w/o reference; running in parallel with large references; new spead-up options: --no-check, --no-gc, --no-snps, --fast</li> <li><strong>Better:&nbsp;</strong>more accurate missasembly detection algorithm, new metrics and reports</li> <li><strong>New MetaQUAST: </strong>better contig binning,<strong>&nbsp;</strong>multi-reference reports,&nbsp;interspecies translocations</li> </ul> <p><a href="https://sourceforge.net/projects/quast/" style="line-height: 1.6em;">Download here</a><span style="line-height: 1.6em;">. Check the full list of </span><a href="http://sourceforge.net/p/quast/wiki/Changes/" style="line-height: 1.6em;">changes here</a><span style="line-height: 1.6em;">.</span></p> Public Tue, 07 Jul 2015 13:20:09 +0000 vlad 496 at https://bioinf.spbau.ru