Alternatives and similar repositories for MentaLiST

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

• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆28Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆49Updated 3 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 3 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• lskatz / lyve-SET
  LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
  ☆26Updated 9 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆32Updated 5 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 2 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆43Updated 2 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆54Updated 3 years ago
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆24Updated 3 years ago
• marbl / harvest
  ☆52Updated 4 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆42Updated last month
• jizhang-nz / fast-GeP
  Fast genealogical relationship evaluation of bacterial isolates with WGS data.
  ☆12Updated 3 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 5 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆53Updated 10 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated 2 months ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 8 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago