De novo assembly

[mihir.karnik]

Hi,

I have been working on a project involving de novo assembly of nucleotides. However, i have run into some problems as the reads that i have been working with are very large in size around 12 GB.
What i wanted to know is that if there is any way i could carry out the assembly by breaking the files into smaller ones and then continuing?
The files i am working on are of the fastq format and i am working on trying to get them to convert them to the fasta format which i believe will be a lot easier to handle.

Please help.

Thanks a lot in advance.

[ECO]

Hello and welcome!

This is probably the wrong forum for this, and is also (sorry!) a very basic question that tells me that you would benefit from searching and reading the many threads that address this very question. If you're still stuck, we need more information (what kind of machine you're running the analysis on would be a start, what program you're using, what organism, other considerations).

Fasta and fastq will not be that different in your handling, except that you're throwing away quality information if you collapse to a fasta.