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
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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
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.
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Check this recent review (Table 2 has lists of lots of useful programs).
There are numerous long-read assemblers available. Many listed here.
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx147/4590140
Do you only have PacBio data? You should get some Illumina:
On stuck records and indel errors; or “stop publishing bad genomes”
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?
From the blog post I linked:
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.