tools for assembling large contigs

[shuang]

I need a tool to assemble very large reads.

I have 2 sets of large contigs, from 454 and Pacbio. The largest contig is 20kb. The average length is 4kb. I'm trying to use those 2 sets of contigs in order to assemble to larger contigs.

(The clone is about 150kb. )

[SES]

I need a tool to assemble very large reads.

I have 2 sets of large contigs, from 454 and Pacbio. The largest contig is 20kb. The average length is 4kb. I'm trying to use those 2 sets of contigs in order to assemble to larger contigs.

(The clone is about 150kb. )

Have a look at minimus2, it has been working well for me. You might also want to read about MSR-CA, which is an assembly pipeline that first constructs very long "super-reads" from sequence reads. Then, overlaps between the super-reads are computed, and you might find that there is a way to incorporate your contigs at this stage.

[flxlex]

The latest version of Celera apparently can accepts reads as large as 32 kb for assembly