Alternatives and similar repositories for srst2

Users that are interested in srst2 are comparing it to the libraries listed below

• AdmiralenOla / Scoary
  Pan-genome wide association studies
  ☆205Updated last year
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆146Updated 2 weeks ago
• sanger-pathogens / ariba
  Antimicrobial Resistance Identification By Assembly
  ☆182Updated 2 years ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated last week
• cmks / DAS_Tool
  DAS Tool
  ☆163Updated last year
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆142Updated 3 weeks ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆208Updated last year
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆164Updated 8 months ago
• genomicsITER / NanoCLUST
  NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  ☆113Updated 2 years ago
• neherlab / pan-genome-analysis
  Processing pipeline for pan-genome visulization and exploration
  ☆142Updated 2 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆249Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆122Updated last week
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆224Updated 2 weeks ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆177Updated 2 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆247Updated 2 weeks ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆164Updated 3 months ago
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆174Updated last week
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆118Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆97Updated last month
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆114Updated 8 months ago
• smaegol / PlasFlow
  Software for prediction of plasmid sequences in metagenomic assemblies
  ☆107Updated 4 years ago
• AnantharamanLab / VIBRANT
  Virus Identification By iteRative ANnoTation
  ☆181Updated last year
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆140Updated this week
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆145Updated last week
• loneknightpy / idba
  ☆131Updated 2 years ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆181Updated 7 months ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆172Updated 4 years ago
• MaestSi / MetONTIIME
  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
  ☆114Updated 9 months ago
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆224Updated 2 months ago