Dear Surya, > Dear Nestor, > I have used them only with Illumina data but I don't recall that they cannot > be used with 454 paired reads. Is it explicitly mentioned anywhere? In this topic there is mentioning of 454: http://seqanswers.com/forums/showthread.php?t=8350 Apart from that, SSPACE is using bowtie with options that exclude any reads even with one mismatch. And this is hardly the truth for 454. Especially unclipped, raw data. > In case you are using Velvet, SOPRA can be run in integration with Velvet > and the authors suggest that is better than running SOPRA separately > post-assembly although I have not tried using it this way (yet). Good luck! > -Surya > On Fri, Jul 15, 2011 at 12:21 PM, Nestor Zaburannyi > <nestor@xxxxxxxxxxxxx>wrote: >> Dear Surya, >> > Hi Nestor, >> > I have had moderate luck with two scaffolders besides the ones already >> > mentioned. You might want to try them out. >> > SSPACE ( >> > >> http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/sspace/ >> > ) >> > SOPRA (http://www.physics.rutgers.edu/~anirvans/SOPRA/) >> > -Surya >> Thanks, already gave SSPACE a try. It is good, pity only for short reads as >> i understand. Will also try also SOPRA. >> > 2011/7/12 Nestor Zaburannyi <nestor@xxxxxxxxxxxxx> >> >> Dear Bastien, >> >> Thanks for your hints. Indeed, dirty hack involving the reversal of both >> MP >> >> read sets helped. >> >> Regards >> >> Nestor >> >> > On Jul 6, 2011, at 23:19 , Nestor Zaburannyi wrote: >> >> >> I have 454 paired data and Illumina Mate-Pair data. It took me some >> time >> >> to figure out that not the Bambus is wrong... Long story short: >> >> > Actually I am not so sure that Bambus is correct :-) >> >> > One thing to keep in mind are the orientation of the pairs and what >> the >> >> scaffolder expects: >> >> > - Sanger pairs are oriented like this: ------> <-------- and >> that >> >> is what Bambus wants per default >> >> > - 454 pairs are originally oriented like this: --------> >> ---------> >> >> but as scaffolders (and MIRA) originally did not expect that, I use a >> trick >> >> by letting sff_extract reverse one sequence so that everything as back >> to >> >> "normal". Nowadays MIRA could also use the forward / forward >> orientation, >> >> but I had not time to change sff_extract. >> >> > - Illumina paired-end reads look like this: --------> <--------- >> >> ... which makes it easy. >> >> > - Illumina mate-pairs look like this: <--------- ----------> >> ... >> >> which again lets scaffolders like Bambus despair as the expect something >> >> different. MIRA does not care there, it can work with that, too. >> >> >> Most of the contigs are not joined properly and we get hundreds of >> >> thousands "Invalid" links with consistent distance between them. >> Something >> >> like: >> >> > Which is a symptom of what I described: mate-pairs are facing >> outwards, >> >> Bambus expects them to face inwards. >> >> > There is no easy solution to this, the simplest one I can think of is >> to >> >> reverse all reads of the Illumina mate-pair set (both sets!) and then >> >> assemble. Should keep Bambus happy. >> >> > Hope that helps, >> >> > Bastien >> >> -- >> >> З повагою, >> >> Nestor mailto:nestor@xxxxxxxxxxxxx >> >> -- >> >> You have received this mail because you are subscribed to the mira_talk >> >> mailing list. For information on how to subscribe or unsubscribe, please >> >> visit http://www.chevreux.org/mira_mailinglists.html >> -- >> З повагою, >> Nestor mailto:nestor@xxxxxxxxxxxxx >> -- >> You have received this mail because you are subscribed to the mira_talk >> mailing list. For information on how to subscribe or unsubscribe, please >> visit http://www.chevreux.org/mira_mailinglists.html -- З повагою, Nestor mailto:nestor@xxxxxxxxxxxxx -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html