HGAP command line protocol ?

[jtchien0925]

Hello everyone,

I'm new to PacBio so I need your help to guide me or give me some suggestions on my de novo assembly project. I'm currently working on a ~23mb genome and I got ~40x coverage from 3 cells. Thus we decided to use HGAP to do assembly.

When I check the official pacbio user guide https://github.com/PacificBioscience...-SMRT-Analysis

It seems strongly encourage to use their portal. However, I wanted to apply those key steps on our cluster machine, 1BLASR, 2PB/dagcon, 3CA/overlap, 4CA/unitigger, 5PB/utgcns, 6Quiver but I cant find any instruction of using command line tools in any sites. So I would like to ask that if anyone knows how to use command line tools to achieve this goal? We have newest smrtanalysis 2.3.0 in our cluster but I cant find CA/overlap and CA/unitigger under our bin, so is there any package that we need to download?

Thank you for answering my question.

JTC

[flxlex]

You could also use PBcR wgs-assembler.sourceforge.net/wiki/index.php?title=PBcR for steps 1-5, and then smrtanalysis from the command line for quiver. I hardly ever use the portal...

[jtchien0925]

Hello flxlex:

I did looked at the link that you gave to me but it seemed its up to dated.
However, PacBio's document, https://github.com/PacificBioscience...-SMRT-Analysis, did not mentioned that CA/overlap and CA/unitigger represent celera assembler....For me, a newbie, it's really pain to learn their technology.

But thank you for your advise.

Best,

JTC

[gconcepcion]

Hello everyone,

I'm new to PacBio so I need your help to guide me or give me some suggestions on my de novo assembly project. I'm currently working on a ~23mb genome and I got ~40x coverage from 3 cells. Thus we decided to use HGAP to do assembly.

When I check the official pacbio user guide https://github.com/PacificBioscience...-SMRT-Analysis

It seems strongly encourage to use their portal. However, I wanted to apply those key steps on our cluster machine, 1BLASR, 2PB/dagcon, 3CA/overlap, 4CA/unitigger, 5PB/utgcns, 6Quiver but I cant find any instruction of using command line tools in any sites. So I would like to ask that if anyone knows how to use command line tools to achieve this goal? We have newest smrtanalysis 2.3.0 in our cluster but I cant find CA/overlap and CA/unitigger under our bin, so is there any package that we need to download?

Thank you for answering my question.

JTC

Try this link:

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.3.0

[rhall]

JTC,
Even though the steps are distinct, it is difficult to run them as individual tasks, given that then data needs to be split and recombine to make the best use of computational resources. Some kind of workflow engine is generally required. To run HGAP without using SMRT Portal / Pipe, make can be used as a light weight workflow engine: https://github.com/PacificBiosciences/smrtmake, or if you are being a little more adventurous the development assembler FALCON includes its own workflow engine: https://github.com/PacificBiosciences/FALCON