hcdenbakker / sepia

Related projects ⓘ

Alternatives and complementary repositories for sepia

• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆42Updated 4 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆52Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆70Updated 2 weeks ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• marbl / harvest
  ☆51Updated 3 years ago
• pha4ge / hAMRonization_workflow
  Harmonization of AMR predictor tool outputs
  ☆21Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆51Updated 2 months ago
• rhysnewell / Lorikeet
  Strain resolver for metagenomics
  ☆68Updated 3 months ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated 6 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆26Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆38Updated 6 months ago
• bede / hostile
  Precise host read removal
  ☆78Updated 3 weeks ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆36Updated 11 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆68Updated last year
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆71Updated 2 months ago
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆64Updated last week
• sirselim / guppy_parameter_optimiser
  A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate
  ☆31Updated 2 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆42Updated 2 weeks ago
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆65Updated last week
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆48Updated 6 months ago
• EvolBioInf / phylonium
  ♥ Fast and Accurate Estimation of Evolutionary Distances
  ☆27Updated 6 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆41Updated last year
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆49Updated this week
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆39Updated 3 months ago
• bcgsc / ntJoin
  🔗Genome assembly scaffolder using minimizer graphs
  ☆82Updated last month