GraphBinGraphBin: Refined binning of metagenomic contigs using assembly graphs
Stars: ✭ 35 (+20.69%)
Binning refinerImproving genome bins through the combination of different binning programs
Stars: ✭ 26 (-10.34%)
AMBERAMBER: Assessment of Metagenome BinnERs
Stars: ✭ 18 (-37.93%)
charcoalRemove contaminated contigs from genomes using k-mers and taxonomies.
Stars: ✭ 32 (+10.34%)
bonsaiBonsai: Fast, flexible taxonomic analysis and classification
Stars: ✭ 66 (+127.59%)
DRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 159 (+448.28%)
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 (-51.72%)
traitarFrom genomes to phenotypes: Traitar, the microbial trait analyzer
Stars: ✭ 41 (+41.38%)
ORNAFast in-silico normalization algorithm for NGS data
Stars: ✭ 21 (-27.59%)
recentrifugeRecentrifuge: robust comparative analysis and contamination removal for metagenomics
Stars: ✭ 79 (+172.41%)
Maaslin2MaAsLin2: Microbiome Multivariate Association with Linear Models
Stars: ✭ 76 (+162.07%)
raptorA fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
Stars: ✭ 37 (+27.59%)
functree-ngAn interactive radial tree for functional hierarchies and omics data visualization
Stars: ✭ 18 (-37.93%)
metacalMetagenomics calibration R package
Stars: ✭ 16 (-44.83%)
miccamicca - MICrobial Community Analysis
Stars: ✭ 19 (-34.48%)
SemiBinNo description or website provided.
Stars: ✭ 25 (-13.79%)
virnetVirNet: A deep attention model for viral reads identification
Stars: ✭ 26 (-10.34%)
microbiomeMarkerR package for microbiome biomarker discovery
Stars: ✭ 89 (+206.9%)
matamMapping-Assisted Targeted-Assembly for Metagenomics
Stars: ✭ 18 (-37.93%)
DAtestCompare different differential abundance and expression methods
Stars: ✭ 34 (+17.24%)
catchA package for designing compact and comprehensive capture probe sets.
Stars: ✭ 55 (+89.66%)
melonnpanModel-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Stars: ✭ 20 (-31.03%)
InSilicoSeq🚀 A sequencing simulator
Stars: ✭ 116 (+300%)
MG-RASTThe MG-RAST Backend -- the API server
Stars: ✭ 39 (+34.48%)
macrelPredict AMPs in (meta)genomes and peptides
Stars: ✭ 34 (+17.24%)
covid-19-signalFiles and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Stars: ✭ 31 (+6.9%)
DeepMAsEDDeep learning for Metagenome Assembly Error Detection
Stars: ✭ 24 (-17.24%)
sunbeamA robust, extensible metagenomics pipeline
Stars: ✭ 143 (+393.1%)
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 (+96.55%)
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 (+20.69%)
MOSCAMeta-Omics Software for Community Analysis
Stars: ✭ 26 (-10.34%)
gargammelgargammel is an ancient DNA simulator
Stars: ✭ 17 (-41.38%)
StrainFLAIRStrain-level abundances estimation in metagenomic samples using variation graphs
Stars: ✭ 23 (-20.69%)
metacherchantNo description or website provided.
Stars: ✭ 19 (-34.48%)
PandExoA Community Tool for Transiting Exoplanet Science with the JWST & HST
Stars: ✭ 23 (-20.69%)
NearbyFind nearby 3D objects in constant time O(1).
Stars: ✭ 85 (+193.1%)
platonIdentification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Stars: ✭ 52 (+79.31%)
mccortexDe novo genome assembly and multisample variant calling
Stars: ✭ 105 (+262.07%)
CONSENTScalable long read self-correction and assembly polishing with multiple sequence alignment
Stars: ✭ 47 (+62.07%)
pufferfishAn efficient index for the colored, compacted, de Bruijn graph
Stars: ✭ 94 (+224.14%)
PlasFlowSoftware for prediction of plasmid sequences in metagenomic assemblies
Stars: ✭ 74 (+155.17%)
redundansRedundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
Stars: ✭ 90 (+210.34%)