Tag: MAGs

Critical assessment of pan-genomics of metagenome-assembled genomes

Abstract Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation,…

Continue Reading Critical assessment of pan-genomics of metagenome-assembled genomes

many reads are not assembled into long contigs

many reads are not assembled into long contigs 2 Hi folks, I am assembling paired-end short metagnenomic reads (150 bp) using metaSpades and Megahit (with default settings). Then I did binning (with various binners and refiners), only 35-40% trimmed clean reads could be mapped to the bins. This is criticized…

Continue Reading many reads are not assembled into long contigs

Dryad Data — Lichen fungi do not depend on the alga for ATP production

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit…

Continue Reading Dryad Data — Lichen fungi do not depend on the alga for ATP production

Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

Continue Reading Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

how to create a custom database (GTDB) ?

how to create a custom database (GTDB) ? 0 Hello I was asked for creating a custom database from GTDB, I just need to incorporate some metagenome assembly genomes (MAGs) to the GTDB database the issue is that I dont know how to do that. the GTDB file “gtdbtk_data.tar.gz” from…

Continue Reading how to create a custom database (GTDB) ?