Question: Taxonomic analysis of metagenomic data
1
gravatar for bird77
3.0 years ago by
bird7760
bird7760 wrote:

How can I quickly calculate the taxonomic distribution of a metagenome (assembled or unassembled data)?

sequence • 900 views
ADD COMMENTlink modified 8 months ago by Shicheng Guo8.3k • written 3.0 years ago by bird7760
2
gravatar for Brian Bushnell
3.0 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

You can do this very quickly (in a few seconds) with BBMap's Sketch tool, which will compare the data to RefSeq:

sendsketch.sh in=reads.fq reads=4m depth

or

sendsketch.sh in=contigs.fa
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Brian Bushnell17k
1
gravatar for Sej Modha
3.0 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

There are a number of k-mer based taxonomic tools available: https://omictools.com/taxonomy-dependent2-category

ADD COMMENTlink written 3.0 years ago by Sej Modha4.7k
0
gravatar for onestop_data
8 months ago by
onestop_data260
onestop_data260 wrote:

What do you mean by Taxonomic analysis? Do you mean taxonomic binning of the sequences or profiling of the sequences?

I wrote a tool in graduate school that uses k-mers and an optimization method for taxonomic profiling of a metagenome dataset in seconds. The tool is named FOCUS and you can learn more about it here. The page also teaches more details about binning and profiling in case you are interested,

ADD COMMENTlink written 8 months ago by onestop_data260
0
gravatar for Shicheng Guo
8 months ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

How about fastq_screen and Diamond?, I prefer Diamond with my experience.

fastq_screen : https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html

Diamond: https://github.com/bbuchfink/diamond and DIAMOND_analysis_counter.py (SAMSA2)

ADD COMMENTlink modified 7 months ago • written 8 months ago by Shicheng Guo8.3k
1

DIAMOND is simply an aligner. If you don't refer to a tool that does not have a database associated to it, it does no good. Maybe you can add some databases and tools which take the DIAMOND output such as MEGAN which takes the DIAMOND output when aligning against the NR/NT database and can give you back the taxonomic and functional analysis.

I talk here more about DIAMOND and Rapsearch2.

ADD REPLYlink modified 7 months ago • written 8 months ago by onestop_data260
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