Alternatives and similar repositories for STing:

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

• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆24Updated 6 months ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago
• lmc297 / bactaxR
  Bacterial taxonomy construction and evaluation in R
  ☆13Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 2 months ago
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆22Updated 2 weeks ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 3 months ago
• NorwegianVeterinaryInstitute / ALPPACA
  A tooL for Prokaryotic Phylogeny And Clustering Analysis
  ☆11Updated 2 months ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 2 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆21Updated last year
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆38Updated 6 months ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 10 months ago
• farhat-lab / fast-lineage-caller
  ☆14Updated 3 years ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 4 months ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 months ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆37Updated last month
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• rrwick / Compare-annotations
  A script for comparing old vs new versions of genome annotations
  ☆20Updated last year
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 9 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• salzberg-lab / bolotie
  SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
  ☆13Updated last year
• bacpop / pp-sketchlib
  Library of sketching functions used by PopPUNK
  ☆30Updated 3 weeks ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• cchauve / HyAsP
  Hybrid Assembler for Plasmids
  ☆10Updated 2 years ago