https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?action=history&feed=atom&title=SAMSWiki%2FWebDocumentation%2FIntroDuction%2FAnaLysis 2026-04-22T08:05:24Z Revision history for this page on the wiki MediaWiki 1.39.7 https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=SAMSWiki/WebDocumentation/IntroDuction/AnaLysis&diff=1362&oldid=prev 2011-10-26T06:15:37Z

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Admin https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=SAMSWiki/WebDocumentation/IntroDuction/AnaLysis&diff=1361&oldid=prev 2006-10-16T07:52:56Z

<p></p> <p><b>New page</b></p><div>__NOTOC__<br /> Analysis using the SAMS pipeline:<br /> <br /> * 1) Pre-processing<br /> <br /> Four steps are used for the pre-processing in SAMS:<br /> <br /> * Quality clipping using PHRED (Q= 13)<br /> * Repeat masking using RepeatMasker where the regions are masked by Xs.<br /> * Vector sequence masking using [http://www.biomax.com/products/harvester/harvester_pp.htm vector clipper].<br /> * Sequences shorter than 50 bp are removed.<br /> * 2) Clustering<br /> <br /> SAMS is using the BioMake tool developped in the group by Thomas Bekel.<br /> <br /> * Performs an all against all BLAST<br /> * Builds a graph according to found overlaps<br /> <br /> The minimum overlap&#039;s length is 40 bp and 95% of required similarity and a maximum number of mismatches of 20 bp. <br /> <br /> * 3) Assembly<br /> <br /> SAMS is using the CAP3 program. Fore more information, please have a look at the CAP3 paragraph.</div>

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