Question: Good Books/Resources to learn metagenomic analysis?
1
gravatar for jimpinney
5 weeks ago by
jimpinney10
UC Merced
jimpinney10 wrote:

I've been searching around to find some good resources on metagenomic shotgun analysis but I can't really find any. I've read the biostars handbook section but it mostly covers 16S analysis. I'm specifically interested in long read (a la Nanopore) metagenomic sequence assembly.

I'm a newbie to this field, and from what I can tell, a generic assembly pipeline would look something like FastQC -> CANU -> some sort of unsupervised binning software -> RACON and then on to classifying and such.

In theory my goal is, I want to be able to go out into the woods with a minION, sequence some random soil bacteria, and be able to tell what bacteria it is, what it does, and also be able to identify any novel bacterial genomes present.

Am I on the right track here and can anyone point me in the direction of good resources, or have advice?

ADD COMMENTlink modified 5 weeks ago by Mensur Dlakic6.4k • written 5 weeks ago by jimpinney10

my last take on this was a workshop discussion 2/3 years ago, when the error rate made it very experimental and a bitchallenging. I guess that still holds true, but this is what it makes exciting, too ;-)

I would fill the gap of the unsupervised binning software with metabat2, classification with Kajiu or Kraken2, but in general I would start with a pipeline close to what you sketched out.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Carambakaracho2.2k
0
gravatar for colindaven
5 weeks ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:

Sounds interesting.

This paper might be useful:

https://www.nature.com/articles/s41598-020-70491-3

  • Assembly - tools already mentioned, + metaflye
  • Polishing
  • Gene finding - prokka etc. Perhaps Maker ?
  • interproscan for protein sequence analysis. Also diamond
  • blastn vs genbank for finding novel contigs without hits
ADD COMMENTlink written 5 weeks ago by colindaven2.3k
0
gravatar for Mensur Dlakic
5 weeks ago by
Mensur Dlakic6.4k
USA
Mensur Dlakic6.4k wrote:

This resource cover all the steps of assembly and annotation:

https://github.com/parfreylab/metagenome_assembly_pipeline

There are links to software tools and recipes for individual steps.

ADD COMMENTlink written 5 weeks ago by Mensur Dlakic6.4k
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