tag:blogger.com,1999:blog-36768584.post5675749549632876982..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Envisioning The Perfect ScaffolderKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-36768584.post-53180181759477595002014-01-27T17:35:44.579-05:002014-01-27T17:35:44.579-05:00Well, in SPAdes scaffolder is (yet) far from being...Well, in SPAdes scaffolder is (yet) far from being perfect. However, one of its strengths is that it is integrated with repeat resolver. And repeat resolver is capable to consume various information about genomic distances (which is converted inside assembler into the set of paths in the graph). So, such an information allows either to resolve a repeat fully, or "jump" over it and thus make a scaffold, or... nothing. but we're working on scaffolding, yes.anton.korobeynikovhttps://www.blogger.com/profile/11466623403187908620noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-11255096118042709042014-01-04T17:00:19.554-05:002014-01-04T17:00:19.554-05:00I used Storify to capture some of the discussion f...I used Storify to <a href="http://storify.com/OmicsOmicsBlog/follow-up-to-envisioning-the-perfect-scaffolder?utm_campaign=&utm_content=storify-pingback&utm_medium=sfy.co-twitter&utm_source=t.co&awesm=sfy.co_sMTA" rel="nofollow">capture some of the discussion</a> from this piece, including links to great blog entries by other authors on the topicKeith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-11917866000966277392014-01-03T14:10:47.158-05:002014-01-03T14:10:47.158-05:00I think the SPAdes guys have done the best work in...I think the SPAdes guys have done the best work in this respect, but someone needs to go into their code to extract out the scaffolder :)homolog.ushttp://homolog.usnoreply@blogger.com