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
  ☆25Updated 2 years ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 6 months ago
• c2-d2 / disty
  Disty McMatrixface - compute a distance matrix from a core genome alignment file
  ☆14Updated 2 years ago
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆20Updated last week
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 3 months ago
• maxibor / sam2lca
  Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
  ☆9Updated 7 months ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated 11 months ago
• TGenNorth / NASP
  Northern Arizona SNP Pipeline
  ☆19Updated 4 months ago
• aweimann / traitar
  ☆22Updated last year
• LanLab / ShigEiFinder
  Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
  ☆11Updated last year
• smangul1 / MiCoP
  MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
  ☆15Updated 2 years ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 9 months ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 2 months ago
• SilvioWeging / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆18Updated last month
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• PROBIC / mSWEEP
  mSWEEP High-resolution sweep metagenomics using fast probabilistic inference
  ☆14Updated 5 months ago
• Askarbek-orakov / ASAR
  Advanced metagenomic Sequence Analysis in R
  ☆15Updated 6 years ago
• sharpton / shotmap
  A Shotgun Metagenome Annotation Pipeline
  ☆23Updated 8 years ago
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated 3 weeks ago
• ansariazim / treeBreaker
  Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree
  ☆25Updated 6 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• scwatts / genome_painter
  Paint genomes with taxa-specific k-mer probabilities
  ☆15Updated 2 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• aesheppard / TETyper
  transposable element typing pipeline
  ☆17Updated last year
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 2 years ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• klebgenomics / Kleborate-viz
  Visualisation application for Klebsiella genotypes generated by Kleborate.
  ☆9Updated 4 years ago
• 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