Best Software For 454/Pacbio Hybrid Assembly

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11.0 years ago

mgalactus ▴ 780

Hi,

is there a software that can effectively combine 454 and PacBio reads in a bacterial genome assembly?

PacBio published a technical note indicating a few options:

SMRTAnalysis (both hybrid and scaffolding)
ALLPATHS-LG
Celera
MIRA

Which software is best suited for this task, considering that this is an average bacterial genome? Are there any other options available?

Thanks

EDIT: here's another possible solution (CELUREAN, pre-print)

assembly bacteria 454 • 3.6k views

ADD COMMENT • link 11.0 years ago by mgalactus ▴ 780

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Are you sure you need 454 reads at all?

You only need 1-2 SMRT cells for a PacBio-only bacterial Assembly according to this dataset on E. Coli. The dataset is from P4-C2 chemistry, which produced a complete assembly using just 1 SMRT Cell using a 20kb size selected library.

The new HGAP2 in SMRT Analysis v2.1 speeds up the assembly process a few fold. You can get the software at the Developer's Network: http://www.pacbiodevnet.com

ADD REPLY • link 11.0 years ago by landolin ▴ 10

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Well, according to FastQC, my PacBio reads have a really low quality (around 10 phred); do you think that that is sufficient for a bacterial assembly?

ADD REPLY • link 11.0 years ago by mgalactus ▴ 780

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