Metagenomics & Community Exploration
Some of the tools in KBase available for analyzing microbial communities and metagenomics
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Some of the tools in KBase available for analyzing microbial communities and metagenomics
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KBase has a multitude of . They provide a way to understand the functional interactions between species in microbial communities. Annotated genomes extracted from metagenomic sequence libraries can be used for metabolic modeling, comparative phylogenomics, functional profiling, and more.
– Raw read quality control and analysis
– Read trimming and adaptor removal
– Taxonomy assignment of raw metagenomic reads
– Assemble large and complex metagenomic reads
– Assemble shotgun metagenomic reads
– Assemble short metagenomic reads
– Group metagenomic contigs using depth-of-coverage, nucleotide composition, and marker genes
– Group metagenomic contigs using strain abundance and nucleotide composition
– Group metagenomic contigs using depth-of-coverage and nucleotide composition
– Optimizes bacterial or archaeal genome bins using a de-replication, aggregation and scoring strategy
– Assess genome and MAG quality
()– Improve and circularize single-genome assemblies and MAGs
() – Visualize assembly coverage
RAST for and – Annotate multiple bacterial or archaeal genomes and assemblies or sets using RASTtk
– Annotates Metagenome Assembled Genomes (MAGs) and provides an interactive functional summary per genome
() – Dereplicate binned contigs, assemblies, and genomes using nucleotide similarity
– Identify viral sequences from viral and microbial metagenomes
– Assign taxonomy to isolate and classify Metagenome Assembled Genomes (MAGs) using Genome Taxonomy Database (GTDB) genome taxonomy
– Generate and merge metabolic models from annotated genomes
– Produce phylogenetic trees from annotated genomes
– analyze community metabolism