Alternatives and similar repositories for PneumoKITy:

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

• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆22Updated 3 weeks ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆41Updated last month
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆32Updated 4 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last month
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆34Updated last month
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 9 months ago
• Kirk3gaard / MicroBench
  Overview of our data for microbial genomic benchmarking
  ☆20Updated this week
• UPHL-BioNGS / Donut_Falls
  Basic workflow for nanopore sequencing data
  ☆16Updated this week
• MicrobialDarkMatter / nanomotif
  Nanomotif - a tool for identifying methylated motifs in metagenomic samples
  ☆25Updated this week
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated this week
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆48Updated 3 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• kwongj / contig-puller
  Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
  ☆13Updated 6 years ago
• scwatts / hicap
  in silico typing of the H. influenzae cap locus
  ☆12Updated 9 months ago
• Public-Health-Bioinformatics / pubmlst_client
  List and download schemes from pubMLST.org and other BIGSDB servers
  ☆10Updated 6 months ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆27Updated 3 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated last week
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆22Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆26Updated 2 weeks ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated last year
• microbinfie-hackathon2020 / CSIS
  Code Safety Inspection Service
  ☆20Updated 2 years ago
• MDU-PHL / emmtyper
  emm Automatic Isolate Labeller
  ☆10Updated last month
• phac-nml / mikrokondo
  A simple pipeline for bacterial assembly and quality control
  ☆17Updated this week
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 6 years ago