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
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆49Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆69Updated this week
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last week
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago
• 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
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆22Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆28Updated 8 months ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆32Updated 5 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆26Updated 2 months ago
• wandreopoulos / deeplasmid
  ☆20Updated 9 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 9 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 3 weeks ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆42Updated 8 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆24Updated 3 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 6 months ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆58Updated 2 months ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• MicrobialDarkMatter / nanomotif
  Nanomotif - a tool for identifying methylated motifs in metagenomic samples
  ☆27Updated last week
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆46Updated 2 months ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆54Updated last month