Alternatives and similar repositories for shigatyper:

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

• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 6 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆22Updated 3 weeks ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 2 months ago
• LanLab / ShigEiFinder
  Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
  ☆11Updated last year
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated 2 weeks ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• appliedbinf / el_gato
  ☆10Updated last week
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks ago
• staphopia / staphopia-sccmec
  Archived - please see updated sccmec tool at link below
  ☆13Updated 7 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 4 months ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆34Updated last month
• MDU-PHL / meningotype
  In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis
  ☆12Updated 2 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last month
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆18Updated 2 years ago
• CFSAN-Biostatistics / bettercallsal
  Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.
  ☆11Updated 3 weeks ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆26Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆25Updated 2 years ago
• centre-pathogen-genomics / snippy-ng
  ☆15Updated 2 weeks ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 6 months ago
• ubinfie / ubinfie.github.io
  µbinfie blog
  ☆17Updated last month
• jonas-fuchs / virHEAT
  Visualize microbial evolution at the SNP level!
  ☆14Updated 5 months ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago