Question: Amplicon Sequencing
0
gravatar for Burnedthumb
8.0 years ago by
Burnedthumb90
Netherlands
Burnedthumb90 wrote:

Hi,

I am looking for an alignment tool that is good at aligning a lot of small amplicon sequences to small reference sequences. I have tried BWA and Bowtie, (and BLAST with a makeshift Perl parser behind it) but can someone point me to another good alignment program for this kind of job?

Kind regards,

bowtie bwa sequencing • 2.6k views
ADD COMMENTlink written 8.0 years ago by Burnedthumb90
3
gravatar for Chris Evelo
8.0 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

In general [?]BLAT[?] is good at dealing with short sequences, and it has been used for amplicon sequences as well. It might be worth a try.

ADD COMMENTlink written 8.0 years ago by Chris Evelo9.9k

I will give this one a try. Thank you very much!

ADD REPLYlink written 8.0 years ago by Burnedthumb90
0
gravatar for Marina Manrique
8.0 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

Are you working with 454 data? If so you could try the Amplicon Variant Analyzer (AVA) tool that comes with 454 machines

http://www.454.com/products-solutions/analysis-tools/gs-amplicon-variant-analyzer.asp

ADD COMMENTlink written 8.0 years ago by Marina Manrique1.3k
0
gravatar for Josh Herr
6.4 years ago by
Josh Herr5.6k
University of Nebraska
Josh Herr5.6k wrote:

I just saw this question, so I'm not sure if you've figured the issue out or not. I'm not sure how long your reference is or how long your amplicon sequences are, or how much variability you see in the amplicons.

I've recommended Julian Catchen's Stacks pipeline to numerous people here already. I'm using it to address population genetic questions with metagenomic amplicon data, but depending on what you are actually doing perhaps our uses aren't very different. Give it a try and see what you think. You'll need to know a bit of MySQL and be confident working in the shell to use it. I generally use the genotypes command in the pipeline and if you read the documentation you can specify which flags to use for that command that will be specific for your data.

ADD COMMENTlink written 6.4 years ago by Josh Herr5.6k
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