Alternatives and similar repositories for PneumoCaT:

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

• ukhsa-collaboration / snapperdb
  ☆24Updated 6 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated 2 months ago
• tseemann / scapper
  Whole genome core alignments from multiple draft genomes
  ☆12Updated 8 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆55Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 months ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 5 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆30Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆34Updated 2 weeks ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 3 months ago
• iferres / pagoo
  A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
  ☆28Updated last year
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• LaborBerlin / score-assemblies
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
  ☆24Updated 9 months ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆34Updated 3 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆19Updated 7 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆40Updated 4 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆55Updated last week
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 7 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆49Updated 6 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆30Updated last month
• agudeloromero / EVEREST
  Viral genome assemble and characterisation
  ☆10Updated last year
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• leaemiliepradier / PlasForest
  A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
  ☆17Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• lskatz / pdtk
  NCBI Pathogen Detection Portal toolkit
  ☆11Updated last year
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆25Updated 3 months ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago