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
  ☆61Updated 2 weeks ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 2 months ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆55Updated 5 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆28Updated 6 months ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆30Updated 2 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 3 years ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• cruizperez / FastAAI
  ☆24Updated 8 months ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆36Updated 11 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 5 months ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 7 months ago
• 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
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 2 months ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆22Updated 2 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated 2 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 8 months ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 2 months ago
• laxeye / zga
  ZGA prokaryotic genome assembly and annotation pipeline
  ☆13Updated last year