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 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