Best Software For 454/Pacbio Hybrid Assembly
0
0
Entering edit mode
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
1
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 1346 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6