Alternatives and similar repositories for emmtyper

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

• UPHL-BioNGS / Donut_Falls
  Assembly of Nanopore Sequencing
  ☆16Updated 3 weeks ago
• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆25Updated 2 months ago
• appliedbinf / el_gato
  ☆10Updated 4 months ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated 3 weeks ago
• GlobalPneumoSeq / gps-pipeline
  Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequ…
  ☆17Updated last week
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆38Updated last week
• jmcbroome / BTE
  Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit
  ☆14Updated 3 months ago
• staphopia / staphopia-sccmec
  Archived - please see updated sccmec tool at link below
  ☆13Updated last year
• microbinfie-hackathon2020 / CSIS
  Code Safety Inspection Service
  ☆20Updated 2 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• lskatz / lyve-SET
  LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
  ☆27Updated last year
• iqbal-lab-org / viridian
  ☆22Updated 5 months ago
• scwatts / hicap
  in silico typing of the H. influenzae cap locus
  ☆12Updated last year
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆60Updated 2 months ago
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆22Updated last year
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated 2 years ago
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆18Updated 3 years ago
• Public-Health-Bioinformatics / pubmlst_client
  List and download schemes from pubMLST.org and other BIGSDB servers
  ☆10Updated 10 months ago
• mbhall88 / ontime
  Extract subsets of ONT (Nanopore) reads based on time
  ☆22Updated 11 months ago
• wslh-bio / dryad
  Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.
  ☆18Updated 2 weeks ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated this week
• phac-nml / rebar
  REcombination BARcode detector.
  ☆16Updated last year
• phac-nml / mikrokondo
  A simple pipeline for bacterial assembly and quality control
  ☆17Updated 2 weeks ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• dportik / LRSW-Taxonomic-Profiling-Tutorial
  Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …
  ☆13Updated 3 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated 2 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆27Updated last month
• ablab / plasmidVerify
  plasmidVerify: plasmid contig verification tool
  ☆13Updated 5 years 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
• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 5 months ago