18 projects
biobakery-workflows
bioBakery workflows: A collection of meta'omic analysis workflows
humann
HUMAnN: The HMP Unified Metabolic Analysis Network, version 3
waafle
WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events
metawibele
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
parathaa
PARATHAA: Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons.
fugassem
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in microbiome
HAllA
HAllA: Hierarchical All-against All Association Testing
MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
PhyloPhlAn
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
kneaddata
anadama2
AnADAMA2: Another Automated Data Analysis Management Application 2
lefse
LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
export2graphlan
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn
graphlan
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *in-vivo* transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.
shortbred
ShortBRED: a system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data
humann2
HUMAnN2: The HMP Unified Metabolic Analysis Network 2
ppanini
PPANINI: Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration.
