cguyomar
commented
2 years ago Hi, MinYS was developped to assemble bacterial symbiotic genomes, especially in the case of holobionts where sequencing data is dominated by host reads. MinYS has not been tested on samples of higher diversity/complexity such as soil metagenomes. In that context, I'm unsure MinYS would be able to assemble very complete genomes, but it could definitely be useful to make partial assemblies and/or improve contiguity in pre-existing assembly. You are welcome to try though, and I'd be curious to see how it goes !
Best, Cervin
Hello, It's appreciated for developing a such amazing tools, which combined reference-based and de novo assembly. It seems that MinYS was developed in the context of mining a particular symbiont genomes, while, I'm wondering: is it applicable for assembly of ordinary particular genomes in soil metagenomes? if it still works well, Will more than one genomes be expected to obtain from a metagenomic sample with a reference genome given as input? or only one genome could be recovered from a metagenomic sample?
I can't wait to apply MinYS in my research, in which I want to recover specific genomes, but with low abundances in soil metagenomes. Looking forward for your response. Thanks!