How do I assemble long and short contigs togeather?

[AndrewRGross]

I'd like to assemble a fasta file of sequences with read lengths varying from 200 - 200,000 bases.

I've assembled 150 bp illumina reads using IDBA-UD. Now I have various files with thousands of contigs. I'd like to organize contigs from different assemblies into bins and then assemble the binned contigs into longer contigs. I don't know how to carry out this assembly.

I only have experience assembling short reads from a sequencing run. I have no idea how to assemble long contigs together. Any ideas?

[AndrewRGross]

I found the answer: Once I've binned the initial assembly, I bin the reads that each contig in each bin is comprised of. Then I re-assemble the original reads, doing each bin separately as its own batch.

[sphil]

have a look at the program FLASH, it might help! It does good work and especially for your task, try to use it after your first initial assembly...