gargammelgargammel is an ancient DNA simulator
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StrainFLAIRStrain-level abundances estimation in metagenomic samples using variation graphs
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metacherchantNo description or website provided.
Stars: ✭ 19 (-26.92%)
MetaCoAGBinning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
Stars: ✭ 29 (+11.54%)
charcoalRemove contaminated contigs from genomes using k-mers and taxonomies.
Stars: ✭ 32 (+23.08%)
bonsaiBonsai: Fast, flexible taxonomic analysis and classification
Stars: ✭ 66 (+153.85%)
DRAMDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 159 (+511.54%)
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 (-46.15%)
traitarFrom genomes to phenotypes: Traitar, the microbial trait analyzer
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ORNAFast in-silico normalization algorithm for NGS data
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recentrifugeRecentrifuge: robust comparative analysis and contamination removal for metagenomics
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Maaslin2MaAsLin2: Microbiome Multivariate Association with Linear Models
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functree-ngAn interactive radial tree for functional hierarchies and omics data visualization
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metacalMetagenomics calibration R package
Stars: ✭ 16 (-38.46%)
miccamicca - MICrobial Community Analysis
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SemiBinNo description or website provided.
Stars: ✭ 25 (-3.85%)
virnetVirNet: A deep attention model for viral reads identification
Stars: ✭ 26 (+0%)
microbiomeMarkerR package for microbiome biomarker discovery
Stars: ✭ 89 (+242.31%)
GraphBinGraphBin: Refined binning of metagenomic contigs using assembly graphs
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matamMapping-Assisted Targeted-Assembly for Metagenomics
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DAtestCompare different differential abundance and expression methods
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catchA package for designing compact and comprehensive capture probe sets.
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Binning refinerImproving genome bins through the combination of different binning programs
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melonnpanModel-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
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InSilicoSeq🚀 A sequencing simulator
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AMBERAMBER: Assessment of Metagenome BinnERs
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MG-RASTThe MG-RAST Backend -- the API server
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macrelPredict AMPs in (meta)genomes and peptides
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covid-19-signalFiles and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
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DeepMAsEDDeep learning for Metagenome Assembly Error Detection
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sunbeamA robust, extensible metagenomics pipeline
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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 (+119.23%)
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 (+34.62%)