Alternatives and similar repositories for bacterial_wgs_training:

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

• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆20Updated 5 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 3 months ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 6 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆55Updated last week
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆27Updated last year
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 8 months ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆25Updated 2 years ago
• apredeus / 10k_genomes
  Various scripts for efficient processing of 10k Salmonella genomes
  ☆14Updated 3 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆39Updated 5 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆40Updated 4 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆26Updated last month
• katholt / RedDog
  ☆36Updated 2 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆24Updated this week
• GunzIvan28 / rMAP
  Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…
  ☆22Updated this week
• klebgenomics / Kleborate-viz
  Visualisation application for Klebsiella genotypes generated by Kleborate.
  ☆9Updated 3 years ago
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆23Updated 6 years ago
• mbhall88 / pistis
  Quality control plotting for long reads
  ☆10Updated 8 months ago
• idolawoye / BAGEP
  A pipeline for Bacterial Whole genome sequence data analysis
  ☆15Updated 2 years ago
• andrewjpage / krocus
  Predict MLST directly from uncorrected long reads
  ☆26Updated 2 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆35Updated 3 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆18Updated 2 years ago
• oschwengers / tadrep
  Targeted Detection and Reconstruction of Plasmids
  ☆20Updated 8 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 6 months ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…
  ☆41Updated last month