CAP3 to merge two assemblies?

[LizBent]

Hi there, I have two assemblies (one from Illumina data made using Trinity, one from 454 data made using Newbler) and I would like to combine them into one assembly. It was suggested that I try CAP3 or Minimus2 for this. CAP3 is available on our local grid as a command line interface, but since I have never used it before I'm not sure how to ask it to process multiple FASTA files. Do I need to concatenate my two assemblies into one file for processing, or is there a CAP3 command line syntax that allows for multiple input files?

Thanks for your help,

Liz

[kmcarr]

Liz,

CAP3 takes a single FASTA file for input so you will need to concatenate your two assemblies.

[pari_89]

Hi, I have used CAP3 with smaller dataset like 616 MB and it worked fine. I am trying to used it with a fasta file of 700 MB and a qual file of aroung 2 GB. I am working on a machine having 79 GB of diskspace and 117 GiB of Memory and 16 cores. The program keeps working and then automatically gets killed without any warning.

Can anyone please help me.

Thank you.

[sklages]

You may also consider using MIRA for this purpose.
You seem to have a transcriptome dataset. You may also consider assembling these two datasets with MIRA from scratch (well, depending on the size of the input data).

http://sourceforge.net/apps/mediawiki/mira-assembler

[pari_89]

You may also consider using MIRA for this purpose.
You seem to have a transcriptome dataset. You may also consider assembling these two datasets with MIRA from scratch (well, depending on the size of the input data).

http://sourceforge.net/apps/mediawiki/mira-assembler

Hi, I am doing a performance evaluation of assemblers and already have mira in my list. I have tried mira and it worked fine but CAP3 does not work and I am left only with CLCworkbench, Newbler, Ray and Mira. If anyone made CAP3 work with a larger dataset, can you please help out.

THank you.