[rskr]

I have a similar problem. I want to combine contigs/scaffolds assembled with different dataset, e.g. sanger,454 and solexa. I wanted to combine them based on Mummer alignments. However, it's so hand for me. The organism is 40M and the largest scaffold is 2M. Can I use these software to finish my job?

Cap3 and Mummer have issues in scaling, besides cap3 is for ESTs anyway.

[anli]

Hi.

I also have come across this issue. I have illumina PE data from an archaea and I now have two datasets were one is done with 100bp read-length and the other one with 150bp.

Doing an assembly on a merged dataset doesn't seem as a good approach, since you can't set multiple k-mer lengths in velvet.

[boetsie]

What do you guys want to do exactly? Do you want to make a consensus of the assemblies, or do you want to extend one of the assemblies by other assemblies?

You should be aware that you can merge repeated regions if they are at the boundaries of the contigs, and thus concatenate distant regions because of the repeat.

Anyway, what you can do is break the assemblies into smaller pieces and do a new denovo. I have a perl script which breaks all assemblies in user-defined k-mers and tries to do a new de novo assembly based on the users 'coverage'. Say you have four assemblies with different k-mers, and you only want to extend a contig by a k-mer if it is supported by e.g. three assemblies.

If you would like to have it, please contact me at [email protected]

Regards,
Boetsie

[edge]

Hi Seth,

I got few question regarding CAP3 might need your advice.
I'm currently facing the following problem when trying to form a single set of non-redundant unigenes by CAP3
I have total of 8 *.fasta right now (RNA-seq scaffold sequence that extracted from same tissue but treated the sample with different condition for sequencing).
I would like to use CAP3 to assemble all the unigenes from different samples (but same tissue just treated the sample with different condition for sequencing) to form a single set of non-redundant unigenes.

Can I know what is the proper command I should apply when running CAP3 in order to form a single set of non-redundant unigenes of my RNA-seq data?
All my 8 sample scaffold in fasta format which is assembled by third party assembler program, Illumina pair-end read, 2X50bp, insert size 200.

This is all the info I have right now.
Many thanks for any advice.

[milo0615]

Hello Mike,

I'm also trying to do this. I think CAP3 might be the best tool but am still exploring this...there is a guy in our department who's written a program using CAP3 to merge velvet and abyss assemblies. It might be of some use. Let me know if you've found any other solutions. You also are in the great state of Oregon...where are you located?

Hi kbushley,

I am also trying to merge six different k-mer assemblies from Abyss. Were you able to merge yours? Can you share the program the guy from your department wrote? Please let me know. I would really appreciate your help.

Thank you,

-Milo

[Brian Bushnell]

To merge multiple assemblies with different kmer lengths, I recommend using Dedupe.