Align Reads from PacBio

Question

[pthom010]

I have a gene of interest (about 3000 bps) in several genotypes of a plant I did PCR on. The PCR products were then sequenced using PacBio sequencing and I received my sequencing reads in a file containing multiple fasta files for each individual genotype. I want to align these reads to get a consensus sequence for the genotype and then compare the consensus sequences with each other. What would be the best program to use and would it be possible to use something with a GUI?

[Chirag Parsania]

Hi, recent issue of nature has very nice article talking about 3rd generation sequencing (e.g PacBio, Oxford nanopore etc. ) and available tools for various bioinformatics analysis. Look in to the Table2 of the article. Probably, you will find the solution.

[lakhujanivijay]

+1 for sharing the article Chirag. Thanks!

Answer 1

[Tm]

You can align your pacbio data with 'bbmap mapPacBio.sh' or 'bwa mem' to reference gene sequence. However, mapPacBio can very well handle raw PacBio reads with high error rates. Have a look at this previous post.

Answer 2

[WouterDeCoster]

I suggest minimap2: https://github.com/lh3/minimap2

and would it be possible to use something with a GUI?

Nope, but a command line is not that bad and it's better to bite the bullet now and spend some time with it to get comfortable. You'll thank yourself in the future.