Question: Align Reads from PacBio
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gravatar for pthom010
12 weeks ago by
pthom0100
pthom0100 wrote:

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?

sequencing alignment • 227 views
ADD COMMENTlink modified 12 weeks ago by WouterDeCoster31k • written 12 weeks ago by pthom0100
2

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by Chirag Parsania930

+1 for sharing the article Chirag. Thanks!

ADD REPLYlink written 12 weeks ago by Vijay Lakhujani3.0k
0
gravatar for toralmanvar
12 weeks ago by
toralmanvar510
toralmanvar510 wrote:

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.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by toralmanvar510
0
gravatar for WouterDeCoster
12 weeks ago by
Belgium
WouterDeCoster31k wrote:

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.

ADD COMMENTlink written 12 weeks ago by WouterDeCoster31k
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