Alternatives and similar repositories for FastMLST

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

• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆60Updated 2 weeks ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated this week
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• CFIA-NCFAD / wgscovplot
  The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…
  ☆19Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• laxeye / zga
  ZGA prokaryotic genome assembly and annotation pipeline
  ☆13Updated last year
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆58Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆48Updated last week
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆39Updated last month
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• cruizperez / FastAAI
  ☆24Updated 7 months ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆21Updated 2 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆25Updated 6 months ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆24Updated last year
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated last month
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆27Updated last month
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated last year
• lmc297 / bactaxR
  Bacterial taxonomy construction and evaluation in R
  ☆13Updated last year
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆30Updated last month
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 3 years ago
• erinyoung / roundabout
  Finding regions of similarity between plasmids
  ☆16Updated 2 years ago