What is the appropriate assembler for PacBio long reads

Question

[bioinforesearchquestions]

Hi folks,

We got long reads sequenced from 10 bacteria using Pac Bio sequencing platform. 5 of them don't have reference bacterial strains and 5 of them have some bacterial strain closer to the subject.

I have to identify anti microbial resistant genes from these 10 bacteria. This is the first time, I am handling PacBio sequence.

Any assembler to handle long reads?As of now don't know the coverage of the sample. Guide me through a reference article if you have encountered for this requirement. I found HGAP from PacBio sequencing platform (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP#implementations).

Celera® Assembler link is broken

[GenoMax]

Check this recent review (Table 2 has lists of lots of useful programs).

[Andy]

There are numerous long-read assemblers available. Many listed here.

https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx147/4590140

[h.mon]

Do you only have PacBio data? You should get some Illumina:

On stuck records and indel errors; or “stop publishing bad genomes”

[bioinforesearchquestions]

As of now, I have been told that I am going to get only the PacBio long reads. Why do you say that I should get some Illumina?

[h.mon]

From the blog post I linked:

If you can’t be bothered reading, then the summary is:

• BOTH single molecule sequencing technologies (PacBio and Nanopore), their major error mode is insertions / deletions

• Once a genome is assembled, some of these errors remain in the assembly

• If they are uncorrected, they inevitably cause a frameshift or premature stop codon in protein-coding regions

• It’s not that you can’t correct these errors, it’s that mostly, outside of the top assembly groups in the world, people don’t

PacBio and Nanopore have insertions / deletions as main error, Illumina doesn't have many insertions / deletions, so you can correct PacBio errors using Illumina reads.

Answer 1

[gconcepcion]

Your best bets are:

HGAP4 (GUI) as a pipeline provided in SMRTLink: https://www.pacb.com/support/software-downloads/

FALCON (command line) (bleeding edge HGAP): http://pb-falcon.readthedocs.io/en/latest/quick_start.html#quick-start

or Canu (command line) basically new Celera Assembler: https://canu.readthedocs.io/en/latest/quick-start.html https://github.com/marbl/canu

[andorjkiss]

I'd stay away from PacBio based assemblers - they're pretty difficult to get to work and take FOREVER. Use a third party assembler, like CANU.