Pacbio scaffolding

[jbingham]

PacBio's software is all open source, BSD license. See pacbiodevnet.com for downloads and links to GitHub projects.

[AdrianP]

This is part of SMRT-pipe. Anyone have any idea how to download that package? Never doing pacbio again..... closed source...

[flxlex]

"AHA (A Hybrid Assembler) uses PacBio's exceptionally long reads to improve existing assemblies and fill in gaps." http://www.pacificbiosciences.com/pr...re/algorithms/. I guess part of smrtpipe software...

[AdrianP]

The way I understand it, is that pb-jelly closes gaps that already exist "NNNNN", but I am interested in building new contigs, or reducing their number.

[mchaisso]

Also: A hybrid approach for the automated finishing of bacterial genomes

http://www.nature.com/nbt/journal/v30/n7/full/nbt.2288.html

PBJelly likely does a better job at getting correct sequences in the gaps, but the hybrid assembler was designed to handle identification of tricky repeat regions and to not misassemble them. The utility may be limited to bacterial sized genomes though.

A snippet from the paper:
To produce the hybrid assembly, we first generated a consensus CDC contig set. Given the clonal nature of the CDC isolates (Supplementary Results), we split contigs from the minimal CDC assembly that were inconsistent with the remaining two isolates. If the split resulted in a subcontig of <1 kb in length, the subcontig was eliminated. We input the resulting 97 contigs in this set, along with 94,526 single-molecule reads from the PacBio RS with an average accuracy of 82.9% (Supplementary Fig. 2), into our hybrid assembly pipeline (Supplementary Fig. 3).

[krobison]

Would PBJelly work?

http://sourceforge.net/p/pb-jelly/wiki/Home/

"PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly’s workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes."

[AdrianP]

I am surprised to not be able to find any scaffolders for pacbio data. I am looking for something that SSPACE does (surprised to see that SSPACE doesn't accept pacbio as input). I have a bunch of contigs generated by velvet, and now I want to link these contigs by using LONG reads, which are pacbio corrected for error.

Honestly, I tried reading how bambus works, they say that it accepts any input from any assembler but they have made it so complicated......