functree-ngAn interactive radial tree for functional hierarchies and omics data visualization
metacalMetagenomics calibration R package
miccamicca - MICrobial Community Analysis
SemiBinNo description or website provided.
virnetVirNet: A deep attention model for viral reads identification
GraphBinGraphBin: Refined binning of metagenomic contigs using assembly graphs
matamMapping-Assisted Targeted-Assembly for Metagenomics
DAtestCompare different differential abundance and expression methods
catchA package for designing compact and comprehensive capture probe sets.
Binning refinerImproving genome bins through the combination of different binning programs
melonnpanModel-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
AMBERAMBER: Assessment of Metagenome BinnERs
MG-RASTThe MG-RAST Backend -- the API server
macrelPredict AMPs in (meta)genomes and peptides
covid-19-signalFiles and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
DeepMAsEDDeep learning for Metagenome Assembly Error Detection
sunbeamA robust, extensible metagenomics pipeline
ganonganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more
kraken-biomCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MOSCAMeta-Omics Software for Community Analysis
gargammelgargammel is an ancient DNA simulator
StrainFLAIRStrain-level abundances estimation in metagenomic samples using variation graphs
MetaCoAGBinning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
charcoalRemove contaminated contigs from genomes using k-mers and taxonomies.
bonsaiBonsai: Fast, flexible taxonomic analysis and classification
DRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
JovianMetagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
traitarFrom genomes to phenotypes: Traitar, the microbial trait analyzer
ORNAFast in-silico normalization algorithm for NGS data
recentrifugeRecentrifuge: robust comparative analysis and contamination removal for metagenomics
Maaslin2MaAsLin2: Microbiome Multivariate Association with Linear Models