sunbeamA robust, extensible metagenomics pipeline
Stars: ✭ 143 (+495.83%)
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
Stars: ✭ 57 (+137.5%)
kraken-biomCreate BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Stars: ✭ 35 (+45.83%)
PlasFlowSoftware for prediction of plasmid sequences in metagenomic assemblies
Stars: ✭ 74 (+208.33%)
MOSCAMeta-Omics Software for Community Analysis
Stars: ✭ 26 (+8.33%)
gargammelgargammel is an ancient DNA simulator
Stars: ✭ 17 (-29.17%)
StrainFLAIRStrain-level abundances estimation in metagenomic samples using variation graphs
Stars: ✭ 23 (-4.17%)
metacherchantNo description or website provided.
Stars: ✭ 19 (-20.83%)
MetaCoAGBinning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
Stars: ✭ 29 (+20.83%)
charcoalRemove contaminated contigs from genomes using k-mers and taxonomies.
Stars: ✭ 32 (+33.33%)
bonsaiBonsai: Fast, flexible taxonomic analysis and classification
Stars: ✭ 66 (+175%)
DRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 159 (+562.5%)
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.
Stars: ✭ 14 (-41.67%)
traitarFrom genomes to phenotypes: Traitar, the microbial trait analyzer
Stars: ✭ 41 (+70.83%)
ORNAFast in-silico normalization algorithm for NGS data
Stars: ✭ 21 (-12.5%)
recentrifugeRecentrifuge: robust comparative analysis and contamination removal for metagenomics
Stars: ✭ 79 (+229.17%)
Maaslin2MaAsLin2: Microbiome Multivariate Association with Linear Models
Stars: ✭ 76 (+216.67%)
functree-ngAn interactive radial tree for functional hierarchies and omics data visualization
Stars: ✭ 18 (-25%)
metacalMetagenomics calibration R package
Stars: ✭ 16 (-33.33%)
miccamicca - MICrobial Community Analysis
Stars: ✭ 19 (-20.83%)
SemiBinNo description or website provided.
Stars: ✭ 25 (+4.17%)
virnetVirNet: A deep attention model for viral reads identification
Stars: ✭ 26 (+8.33%)
microbiomeMarkerR package for microbiome biomarker discovery
Stars: ✭ 89 (+270.83%)
GraphBinGraphBin: Refined binning of metagenomic contigs using assembly graphs
Stars: ✭ 35 (+45.83%)
matamMapping-Assisted Targeted-Assembly for Metagenomics
Stars: ✭ 18 (-25%)
DAtestCompare different differential abundance and expression methods
Stars: ✭ 34 (+41.67%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+129.17%)
Binning refinerImproving genome bins through the combination of different binning programs
Stars: ✭ 26 (+8.33%)
melonnpanModel-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Stars: ✭ 20 (-16.67%)
InSilicoSeq🚀 A sequencing simulator
Stars: ✭ 116 (+383.33%)
AMBERAMBER: Assessment of Metagenome BinnERs
Stars: ✭ 18 (-25%)
MG-RASTThe MG-RAST Backend -- the API server
Stars: ✭ 39 (+62.5%)
macrelPredict AMPs in (meta)genomes and peptides
Stars: ✭ 34 (+41.67%)
covid-19-signalFiles and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Stars: ✭ 31 (+29.17%)