Alternatives and similar repositories for taxonomy-tools

Users that are interested in taxonomy-tools are comparing it to the libraries listed below

• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 2 years ago
• c2-d2 / disty
  Disty McMatrixface - compute a distance matrix from a core genome alignment file
  ☆14Updated 2 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆23Updated last year
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆13Updated last year
• TGenNorth / NASP
  Northern Arizona SNP Pipeline
  ☆20Updated 11 months ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 8 months ago
• smangul1 / MiCoP
  MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
  ☆15Updated 3 years ago
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated 7 months ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 10 months ago
• SwingOlive / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated 2 years ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆18Updated 8 months ago
• phac-nml / neptune
  Neptune: Genomic Signature Discovery
  ☆20Updated 10 months ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 7 months ago
• mmpust / raspir
  Raspir, the rare species identifier
  ☆11Updated last year
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆12Updated last year
• ewissel / hAMRoaster
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Updated last year
• Microbiology / ccontigs
  Detect contigs of complete circular genomes
  ☆23Updated 6 years ago
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• scwatts / genome_painter
  Paint genomes with taxa-specific k-mer probabilities
  ☆15Updated 3 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• ncbi-gpipe / pgap
  (Obsolete) NCBI Prokaryotic Genome Annotation Pipeline. New site:
  ☆16Updated 7 years ago
• jsevo / taxumap
  ☆16Updated 2 years ago
• CAMI-challenge / CAMITAX
  CAMITAX: Taxon labels for microbial genomes
  ☆30Updated last year
• phiweger / uv
  Finding prophage regions in bacterial genomes using brute force
  ☆21Updated 2 years ago
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆16Updated last year
• Gardner-BinfLab / deltaBS
  Quantifying the significance of genetic variation using probabilistic profile-based methods.
  ☆19Updated 4 years ago