HGAP Advanced Protocol

[skerker]

I'm trying to install the HGAP_Assembly_Advanced.1 protocol - I added the necessary .XML file, but when I run the SMRT portal, I'm unable to make any selections on parameters. Wondering if anyone has experience with trying the advanced protocol that lets you work with genomes > 10 Mbp.

I'm following this direction:

Following is a sample HGAP_Assembly_Advanced.1.xml file which should be copied into the ../common/protocols/ directory to display as an option in SMRT Portal v2.0:

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP-2.0

Thanks!
Jeff

[skerker]

Well I figured out the problem -- the .XML file is written for SMRT portal v 2.0 and puts together protocols that no longer exist in the current version of SMRT portal. So it seems that the ability to assemble genomes greater than 10,000,000 doesn't exist?

For example, the advanced protocol tries to call:

<value>common/protocols/assembly/PreAssemblerHGAP.1.xml</value>
<value>common/protocols/assembly/CeleraAssemblerHGAP.1.xml</value>
<select multiple="true">

These .XML files no longer exist in the latest version and CA 7.0 is no used. If anyone has any thoughts on how to use HGAP for > 10Mbp, that would be great.

Thanks again

[skerker]

My mistake -- the wiki docs were confusing. HGAP2 already supports genomes up to 130 Mbp. so adding the advanced HGAP protocol isn't necessary in SMRT portal v 2.1 and higher.

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP