Alternatives and similar repositories for staphb_toolkit:

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

• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆40Updated 4 years ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆42Updated 5 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆34Updated 2 weeks ago
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 2 years ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 6 months ago
• theiagen / public_health_bacterial_genomics
  ☆27Updated last year
• pha4ge / hAMRonization_workflow
  Harmonization of AMR predictor tool outputs
  ☆22Updated 2 weeks ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆30Updated 5 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆26Updated last month
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated last year
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆35Updated 3 months ago
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆25Updated this week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆43Updated 4 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆30Updated 6 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆57Updated last year
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆37Updated last year
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated this week
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆55Updated last week
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆23Updated last year
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆47Updated 3 years ago
• SamStudio8 / dehumanizer
  rapidly rid reads of horrid humans
  ☆15Updated 3 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆28Updated 2 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated last year
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆45Updated 2 years ago