Contig Extraction From .Ace File

Question

[zimmlerten]

Hi all! I have assembled together 10 metagenomic datasets using CAP3. I need to extract specific contigs generated with specific samples. For instance, I need to extract the contigs generated using reads from dataset 1, the ones generated using reads from dataset 3, and so on, without taking into account contigs created by single samples. I want to see which samples shared reads and what contigs are created by shared reads. How can I do it? Best

Michael

Answer 1

[Ketil]

There are probably plenty of tools and scripts floating around to help you do this. I wrote

http://hackage.haskell.org/package/clustertools

You can use ace2contigs to extract the contig sequences, and ace2clusters to get the clustering (i.e. which reads map to which contigs). I used this on CAP3, so it should be compatible with any quirks.

[Raghav]

Dear Ketil, clustertools looking very cool, I have downloaded it and Ieksah to run it [but I unable to run it ] I am specially looking for those clusters which included more than 10 reads in .ace file which is generated by cap3. how do I parse my .ace file through this clustertools. thank you