http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_2.0/quick_start_guide "*Caveat:* Bambus is still being actively developed and the code is currently in the "user beware" and "for experts only" stage. " "*Note:* since Bambus is still under active development you should pull the latest unofficial release of AMOS directly from the CVS repository - see instructions at: Programmer's guide<http://sourceforge.net/apps/mediawiki/amos/index.php?title=Programmer%27s_guide>. " I'll wait for Bambusversionthatdoesn'tsuck. Sincerely yours, Robin On Wed, Jul 6, 2011 at 4:27 PM, WATSON Mick <mick.watson@xxxxxxxxxxxxxxx>wrote: > And Bambus 2? > > Sent from Samsung Mobile > > > Robin Kramer <kodream@xxxxxxxxx> wrote: > > > I have had a very difficult time getting Bambus to scale to Illumina Paired > end scales. I was determined enough to rewrite all of the perl conversion > scripts, simply to realize that the core c++ program gromit will crash very > unexpectedly, and if debug the C++ code you will find that the results are > very suspect, possible do to a non-scaling design, or maybe some > implementation flaw, and the project has been non-active for six years, and > there is no one answering the help messages for Bambus, though the AMOS > project is still active. > > Sincerely yours, > > Robin > > > 2011/7/6 Nestor Zaburannyi <nestor@xxxxxxxxxxxxx<mailto: > nestor@xxxxxxxxxxxxx>> > Dear all. Excuse me for a long letter. > > It seems i am following many steps of Juan specifically from this thread, > but i am opening new one as suggested: > //www.freelists.org/post/mira_talk/fn-in-pairedend-reads,4 > > > 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: > > When i use all the data and both pairing schemes, MIRA result is > outstanding, but Bambus, depending on several factors which i can present, > either crashes or chokes for DAYS on contigs constructed by MIRA. > > These are ridiculous results from bambus when using both pairing schemes. > Note the "203415" number. > > Library: lib_roche_4kb > no. valid links: 2124 > no. incorrect len. links: 281 > no. incorrect ori. links: 13 > no. unchecked links: 715 > > Library: lib_illumina_4kb > no. valid links: 613 > no. incorrect len. links: 203415 > no. incorrect ori. links: 9 > no. unchecked links: 408 > > > Most of the contigs are not joined properly and we get hundreds of > thousands "Invalid" links with consistent distance between them. Something > like: > > contig_c46 (260871, 277262) ====> v:93 l:1382 o:0 ====> contig_c33 (277800, > 308449) > ... > Invalid length: > library lib_illumina_4kb: > 5:117:14385:3543/1 16063 16113 <--- ... 4435 ... ---> 3619 > 3669 5:117:14385:3543/2 > 5:33:7647:14602/1 15968 16018 <--- ... 4702 ... ---> 3791 > 3841 5:33:7647:14602/2 > 5:33:8278:18410/1 16134 16184 <--- ... 4736 ... ---> 3991 > 4041 5:33:8278:18410/2 > 5:47:1673:4256/1 15946<tel:4256%2F1%20%20%2015946> 15996 <--- ... > 4660 ... ---> 3727 3777 5:47:1673:4256/2 > 5:11:1902:7439/2 14782 14832 <--- ... 4721 ... ---> 2624 > 2663 5:11:1902:7439/1 > 5:35:18689:20790/1 14758 14808 <--- ... 4323 ... ---> 2202 > 2244 5:35:18689:20790/2 > 5:9:8606:11124/1 15673 15723 <--- ... 5317 ... ---> 4111 > 4161 5:9:8606:11124/2 > 5:50:8824:11116/2 15738 15788 <--- ... 4299 ... ---> 3158 > 3208 5:50:8824:11116/1 > ... > > Now, i tried to assemble subset of the data in three combinations: > 1- only PE information used > 2- only MP information used > 3- without any template information > > Results of MIRA assembly are absolutely comparable, but take a look at > bambus result: > > 1: > > Library: lib_roche_4kb > no. valid links: 5746 > no. incorrect len. links: 984 > no. incorrect ori. links: 4 > no. unchecked links: 284 > > Library: lib_illumina_4kb > no. valid links: 479 > no. incorrect len. links: 19346 > no. incorrect ori. links: 1 > no. unchecked links: 115 > > 2: > > Library: lib_roche_4kb > no. valid links: 569 > no. incorrect len. links: 23 > no. incorrect ori. links: 16 > no. unchecked links: 87 > > Library: lib_illumina_4kb > no. valid links: 5303 > no. incorrect len. links: 404 > no. incorrect ori. links: 21 > no. unchecked links: 231 > > 3: > > Library: lib_roche_4kb > no. valid links: 632 > no. incorrect len. links: 13 > no. incorrect ori. links: 16 > no. unchecked links: 75 > > Library: lib_illumina_4kb > no. valid links: 5785 > no. incorrect len. links: 274 > no. incorrect ori. links: 32 > no. unchecked links: 271 > > > As you can see, using 454 paired-end information for MIRA assembly results > in the disaster downstream. Please, correct me if i am wrong. > > > Sincerely yours > Nestor > > > -- > 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 > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > -- > 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 >