Alternatives and similar repositories for taxtriage

Users that are interested in taxtriage are comparing it to the libraries listed below

• simonrharris / SKA
  Split Kmer Analysis
  ☆67Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 4 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 3 weeks ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 11 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 2 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 4 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆43Updated 5 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 4 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆32Updated last week
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆41Updated 2 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 4 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆52Updated 4 years ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆29Updated 2 months ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆58Updated 3 months ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆29Updated 6 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 6 years ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 10 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 9 months ago
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆39Updated last year
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated last week
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆34Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated 2 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆49Updated this week
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆38Updated 3 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆44Updated 9 months ago