Alternatives and similar repositories for snippy-ng

Users that are interested in snippy-ng are comparing it to the libraries listed below

• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆22Updated 2 months ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆62Updated last month
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆46Updated last month
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆55Updated 6 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 3 months ago
• lskatz / fundamentals-of-bioinformatics
  ☆27Updated 5 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆63Updated 4 months ago
• phac-nml / rebar
  REcombination BARcode detector.
  ☆16Updated last year
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 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
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 3 months ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆31Updated 3 months ago
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆18Updated 3 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆25Updated last week
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆100Updated last month
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• treangenlab / lemur
  Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
  ☆24Updated 3 months ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆20Updated 9 months ago
• cruizperez / FastAAI
  ☆24Updated 9 months ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆40Updated 2 months 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
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 8 months ago
• mbhall88 / ontime
  Extract subsets of ONT (Nanopore) reads based on time
  ☆23Updated last year
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated last week
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 6 months ago