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FALCON FALCON Unzip "For Phased Diploid Genome Assembly with Single Molecule Real Time Sequencing"

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Jason Chin edited this page Jun 4, 2016 · 3 revisions

A manuscript for demonstrating and evaluating FALCON/FALCON-Unzip for diploid genome assembly is available in BioRxiv (http://biorxiv.org/content/early/2016/06/03/056887). The manuscript also includes the technical details of the underlying ideas and algorithms used for assembling diploid genomes.

You can obtain the data sets used as for the manuscript:

Arabidopsis data: PRJNA314706

V. vinifera cv. Cabernet Sauvignon: PRJNA316730

Clavicorona pyxidata: Upload to SRA in progress. A copy is in the AWS EBS volume as example for an end-to-end run (see below)

The assembly results can be downloaded:

https://downloads.pacbcloud.com/public/dataset/PhasedDiploidAsmPaperData/FUNZIP-PhasedDiploidAssemblies.tgz

Note that both FALCON/FALCON-Unzip are actively under development so the assemblies presented are obtained with the code from earlier revisions. The repository URLs, revisions, and git tagged revisions used for the paper is listed below. We will ensure the master head revision between FALCON/FALCON-Unzip compatible and will likely eventual integrate the two repositories. If you like to try it for now, you should follow the instructions in the FALCON-Integrate repository to install and install FALCON-Unzip with git clone and python setup.py in your environment.

FALCON-Integrate: 
URL: https://github.com/PacificBiosciences/FALCON.git
Git Revision: ffbc609057741896dbe9d09f65bc5c8ef8d57f5a
Git Tag: https://github.com/PacificBiosciences/FALCON-integrate/tree/funzip_052016

FALCON: 
URL: git://github.com/PacificBiosciences/FALCON.git
Git Revision: a1dd4d45bbe0144842cabdd378c46278744231f7
Git Tag: https://github.com/PacificBiosciences/FALCON/tree/funzip_052016

Daligner: 
URL: git://github.com/PacificBiosciences/DALIGNER.git
Git Revision: 029bfa8a40b456bad5499f6e456e6a215bfd307c

DAZZ_DB: 
URL: git://github.com/PacificBiosciences/DAZZ_DB.git
Git Revision: ed0b85e6f14dc394fbabd0731187f98e08a79a0a

pypeFLOW: 
URL: git://github.com/PacificBiosciences/pypeFLOW.git 
Git Revision: e880e2b3cebe7ae19f3101a497a0a8cc6685588e

FALCON-Unzip: 
URL:  https://github.com/PacificBiosciences/FALCON_unzip
Git Revision: 21b1df3491e3bb7b9d8ecd13fc0c9c1a45b6393f
Git Tag:  https://github.com/PacificBiosciences/FALCON_unzip/tree/funzip_052016

Currently, the FALCON-Unzip is only tested with limited cluster computational environments. If you would be interested to see it running without going through configuring it correctly for your own environment, you can try an AWS instance that we build to run FALCON/FALCON-Unzip is a local node mode for the Clavicorona pyxidata data set. Please check https://speakerdeck.com/jchin/example-running-falcon-unzip-on-aws for step-by-step work through to run an example on AWS.

Jason Chin, Jun 2016

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