Alternatives and similar repositories for pyMLST:

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

• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆56Updated last week
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆60Updated last month
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆59Updated 2 weeks ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated 10 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated 2 weeks ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆38Updated 4 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆39Updated 5 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated this week
• wandreopoulos / deeplasmid
  ☆20Updated 6 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated last year
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆62Updated 2 years ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆44Updated 3 weeks ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• MicrobialDarkMatter / nanomotif
  Nanomotif - a tool for identifying methylated motifs in metagenomic samples
  ☆25Updated last week
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆37Updated this week
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆45Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 2 months ago
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆31Updated 2 years ago