Assembling single genomen from metagenome with reference

[cyanoevo]

Hi seqanswers,

Can anyone recommend an assembler for generating a single draft genome from a metagenome (Illumina 2500 pe reads) when a fairly good reference for the genome of interest is available?

My current approach is to do a denovo assembly using SPades and then rearrange the contigs against the reference using MAUVE, was wondering if there were any other options out there?

Cheers
N

[cyanoevo]

And on a related note, what would be the best way to drop contigs that don't align to the reference?

[cyanoevo]

Have come up with another way - map pre-assembled contigs using ABACUS/Contiguator which automatically drops non-aligned contigs .