Question: Install HGAP for de novo PacBio Assembly
0
gravatar for dahliashvets
3.7 years ago by
dahliashvets10
United States
dahliashvets10 wrote:

Hi, I am about to receive pac bio data and need to perform de novo assembly on the data.

I am looking into using HGAP from the Smrt Analysis package. However, this package is absolutely huge according to what I have found online (1TB?).

I only want to use HGAP. Is there anyway to JUST download HGAP, without installing the giant Smart Analysis package? If anyone could help me at all it would be much appreciated, thank you! (Or point me toward a different software for de novo assembly from pac bio data). 

ADD COMMENTlink modified 3.7 years ago by rhall160 • written 3.7 years ago by dahliashvets10
2

You can run SMRT Portal on the Amazon Cloud using a public machine image that Pacific Biosciences maintains and upgrades - you pay only for the machine time that you use.  - link

ADD REPLYlink written 3.7 years ago by rtliu2.0k

Thank you for this information! Much appreciated!

ADD REPLYlink written 3.7 years ago by dahliashvets10

If you are still into this, just to confirm: the actual size of fresh Linux installation of smrtanalysis v2.3 is 3.8G. Maybe worth giving it a shot.

ADD REPLYlink written 2.8 years ago by mjp10
2
gravatar for lexnederbragt
3.7 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

You could consider using PBcR http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR, this is part of the Celera assembler, meaning an easier install. It is also faster (replaces HGAP with MHAp approach).

The drawback is that you'll need to do the quiver polishing yourself, which gets you back to installing either smrtanalysis, or for large datasets, pbalign: https://github.com/PacificBiosciences/pbalign/wiki/Tutorial:-How-to-divide-and-conquer-large-datasets-using-pbalign

 

ADD COMMENTlink written 3.7 years ago by lexnederbragt1.2k

Thank you for your help and advice, much appreciated!

ADD REPLYlink written 3.7 years ago by dahliashvets10
0
gravatar for mjhsieh
3.7 years ago by
mjhsieh0
United States
mjhsieh0 wrote:
$ du -sh smrtanalysis*
179M    smrtanalysis-patch_2.3.0.140936.p4.run
4.0K    smrtanalysis-patch_2.3.0.140936.p4.run.md5
1.1G    smrtanalysis_2.3.0.140936.run
4.0K    smrtanalysis_2.3.0.140936.run.md5
Not 1TB.
ADD COMMENTlink written 3.7 years ago by mjhsieh0
0
gravatar for mjhsieh
3.7 years ago by
mjhsieh0
United States
mjhsieh0 wrote:

For more information, you can start from this page. http://www.pacb.com/devnet/

ADD COMMENTlink written 3.7 years ago by mjhsieh0

Please don't point me to articles that don't actually answer my question. It states here in the manual that you cannot install Smart Analysis on a Mac and it can require up to 10TB of space, and not to install it on a single node machine:

https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation-v2.3.0#installation-guide

So how are most people using HGAP?

I am still looking for anyone who has found a way to download and install just HGAP. 

Thanks. 

ADD REPLYlink written 3.7 years ago by dahliashvets10

I only answered the installation question, not trying to design your experiments. The 10TB of space is an anticipation of data size for a generally big project, not software installation. You will need to have a linux virtual machine on your machine for very small pilot testings. And then start to look into the cloud offering.

ADD REPLYlink written 3.7 years ago by mjhsieh0
0
gravatar for rhall
3.7 years ago by
rhall160
United States
rhall160 wrote:

How large is the genome you intend assembling? For small genomes HGAP in smrtanalysis offers an end to end solution, and is the easiest way to get a 'quiver' polished assembly. HGAP isn't a single executable, it is a pipeline and make use of a large portion of smrtanalysis, it is therefore not possible to just install 'HGAP'.

For a commercial solution you may want to try CLC Bio  http://clcsupport.com/genomefinishing/current/index.php?manual=PacBio_De_Novo_Assembly_Pipeline_beta.html

ADD COMMENTlink written 3.7 years ago by rhall160
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