Tag: MAGs
Nitrogen cycling and microbial cooperation in the terrestrial subsurface
Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…
Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation
Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…
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,…
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…
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…
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…
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…
