# Metagenomics & Community Exploration

KBase has a multitude of [Apps designed to analyze microbial communities and metagenomic reads data](https://kbase.us/applist/#Microbial%20Communities). 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.

### **Metagenomic Read Analysis & Assembly**

* [FastQC](https://kbase.us/applist/apps/kb_fastqc/runFastQC/release)  – Raw read quality control and analysis 
* [Trim Reads with Trimmomatic](https://kbase.us/applist/apps/kb_trimmomatic/run_trimmomatic/release) – Read trimming and adaptor removal
* [Kaiju](https://kbase.us/applist/apps/kb_kaiju/run_kaiju/release) – Taxonomy assignment of raw metagenomic reads
* [MEGAHIT](https://kbase.us/applist/apps/MEGAHIT/run_megahit/release) – Assemble large and complex metagenomic reads
* [MetaSPAdes](https://kbase.us/applist/apps/kb_SPAdes/run_metaSPAdes/release) – Assemble shotgun metagenomic reads
* [IDBA-UD](https://kbase.us/applist/apps/kb_IDBA/run_idba_ud/release) – Assemble short metagenomic reads

### Contig Binning, Optimization, and Quality Analysis 

* [MaxBin2](https://kbase.us/applist/apps/kb_maxbin/run_maxbin2/release) – Group metagenomic contigs using depth-of-coverage, nucleotide composition, and marker genes
* [MetaBAT2](https://kbase.us/applist/apps/metabat/run_metabat/release) – Group metagenomic contigs using strain abundance and nucleotide composition
* [CONCOCT](https://kbase.us/applist/apps/kb_concoct/run_kb_concoct/release) – Group metagenomic contigs using depth-of-coverage and nucleotide composition
* [DAS-Tool](https://kbase.us/applist/apps/kb_das_tool/run_kb_das_tool/release) – Optimizes bacterial or archaeal genome bins using a de-replication, aggregation and scoring strategy
* [CheckM ](https://kbase.us/applist/apps/kb_Msuite/run_checkM_lineage_wf/release)– Assess genome and MAG quality
* [Jorg](https://kbase.us/applist/apps/kb_jorg/run_kb_jorg/beta) ([in beta](https://docs.kbase.us/apps/beta))– Improve and circularize single-genome assemblies and MAGs
* [Circos](https://kbase.us/applist/apps/kb_circos/run_kb_circos/beta) ([in beta](https://docs.kbase.us/apps/beta)) – Visualize assembly coverage 

### **Community Exploration**

* RAST for [Multiple Microbial Genomes](https://kbase.us/applist/apps/RAST_SDK/reannotate_microbial_genomes/release) and [Multiple Microbial Assemblies](https://kbase.us/applist/apps/RAST_SDK/annotate_contigsets/release) – Annotate multiple bacterial or archaeal genomes and assemblies or sets using RASTtk
* [Annotate and Distill Genomes with DRAM](https://kbase.us/applist/apps/kb_DRAM/run_kb_dram_annotate/release) – Annotates Metagenome Assembled Genomes (MAGs) and provides an interactive functional summary per genome
* [dRep](https://kbase.us/applist/apps/kb_dRep/run_dereplicate/beta) ([in beta](https://docs.kbase.us/apps/beta)) – Dereplicate binned contigs, assemblies, and genomes using nucleotide similarity 
* [VirSorter](https://kbase.us/applist/apps/VirSorter/run_VirSorter/release) – Identify viral sequences from viral and microbial metagenomes
* [Classify Microbes with GTDB-Tk](https://kbase.us/applist/apps/kb_gtdbtk/run_kb_gtdbtk_classify_wf/release)  – Assign taxonomy to isolate and classify Metagenome Assembled Genomes (MAGs) using Genome Taxonomy Database (GTDB) genome taxonomy
* [ModelSEED](https://kbase.us/applist/apps/fba_tools/build_multiple_metabolic_models/release) – Generate and merge metabolic models from annotated genomes
* [Phylogenetic Pangenome Accumulation](https://kbase.us/applist/apps/kb_phylogenomics/view_pan_phylo/release) – Produce phylogenetic trees from annotated genomes
* [Metabolic modeling tools for microbial communities](https://docs.kbase.us/apps/metabolic-modeling#microbial-communities) – analyze community metabolism