My first metagenomics project

[Darwin's intern]

I'm brand-new to metagenomics, coming from a 16S microbiome background, and I'm aiming to assemble a microbe's genome from Illumina data. My dream? compare it to public genomes, build a phylogeny, and see if human strains group closer than environmental ones

 

[Josef_10]

Wow, that's a bit of a leap from 16S, but you're in for a treat! Assembling a single microbial genome from a complex metagenome is a cool but tricky project. What kind of microbe are you hoping to assemble?

 

[Emali_day]

Start with quality trimming (Trimmomatic/fastp), assemble with SPAdes or MEGAHIT, then bin with MetaBAT2 or MaxBin. Check completeness with CheckM, compare genomes using ANI (FastANI), and build phylogenies with IQ-TREE. You should see human vs. environmental clustering after that

Hope this straightforward answer helps