Install HGAP for de novo PacBio Assembly

Question

[dahliashvets]

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).

[rtliu]

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

[dahliashvets]

Thank you for this information! Much appreciated!

[mjp]

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.

Answer 1

[lexnederbragt]

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

[dahliashvets]

Thank you for your help and advice, much appreciated!

Answer 2

[mjhsieh]

$ 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.

[mjhsieh]

For more information, you can start from this page.

[dahliashvets]

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

[mjhsieh]

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.

Answer 3

[rhall]

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