Question: Pacbio Metagenome alignment
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gravatar for 934963534
2.5 years ago by
93496353420
93496353420 wrote:

Can I use bwa to align metagenome pacbio reads to several reference genome? Or are there any other tools to achieve metagenome alignment for pacbio reads?

alignment sequence • 839 views
ADD COMMENTlink modified 2.2 years ago by drkennetz500 • written 2.5 years ago by 93496353420

If you already know the genome(s) that could be present in your sample then you can use minimap2 to align reads to the genome(s).

Another approach would be to carry out denovo assembly using canu and then search the contigs against reference databases using either BLAST or DIAMOND.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Sej Modha4.7k
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gravatar for drkennetz
2.2 years ago by
drkennetz500
drkennetz500 wrote:

You don't use bwa to run against multiple genomes at once, but you could of course manually align your sequencing data to multiple genomes 1 by 1 using bwa mem or minimap2. Furthermore, for actual metagenome alignment tools, I would look at this paper:

http://ccb.jhu.edu/people/salzberg/docs/Breitwieser-etal-2017-Metagenomics-review-reprint.pdf

As your question is more complicated than a simple yes or no. To do what you are asking properly there are several things to take into account (which are all discussed in this review).

You will want to look at the readQC metrics as well as the metagenome alignment section (and maybe even metagenome assembly).

ADD COMMENTlink written 2.2 years ago by drkennetz500
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