how to order the contigs

[luckylove]

when I sequence a genome de nove sequencing, how can I certain the sequence of the contigs, For example, there are contig A, contig B, contig C and how can I know which contig is in the front of others, which is the second and who is the last one?
I know maybe the software of Manuve can do this. Is there any other software can do this too?
Thank you!

[flxlex]

Moved to a more appropriate forum. Also, this question has been asked multiple times, please search the forums...

[pag]

I'd recommend searching the forum in addition to below

the only way to be certain of contig order is to have the whole genome sequenced and a total number of contigs equal to the number of chromosomes+plasmids in your organism!


Other than that, you can predict scaffolds based on blasting all your contigs against the "nr" database, finding the typically most closely related organism, then blasting all contigs against ONLY that organism.

Then play around with contig order to minimize the number of genomic inversions and other changes at the ends of contigs and arrange them using a tool like ACT. You can use this information to predict which primer pairs you need for gap closure. If things are ambiguous, try multiple different contig orders and/or skip over a contig in the middle to determine contigs that flank the ambiguously placed contig (which could be a duplicate).

There may be an automated way to do the ACT-like step, but I'm personally not aware of it.

[luckylove]

thank you for your reply. your idea is useful to me and i will try. in fact i have used Manuve to do the job, but the Manuve come across some trouble and i can not solve them, so i hope change a new software.

[pag]

http://www.sanger.ac.uk/resources/software/act/ is what I used

[krobison]

There are comparative assemblers / scaffolders as part of the AMOS suite.

Do you have a link for "Manuve"? I can't find it

[gaffa]

There are comparative assemblers / scaffolders as part of the AMOS suite.

Do you have a link for "Manuve"? I can't find it

luckylove problably means "Mauve": http://gel.ahabs.wisc.edu/mauve/