Alternatives and similar repositories for staphb_toolkit

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

• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated last year
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• fmalmeida / MpGAP
  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
  ☆63Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 2 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆31Updated last year
• jlumpe / gambit
  A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
  ☆34Updated 11 months ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆44Updated last month
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated this week
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆29Updated 3 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated last month
• UPHL-BioNGS / Grandeur
  UPHL's Reference Free Pipeline
  ☆27Updated 3 weeks ago
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• angelovangel / nxf-kraken2
  A simple nextflow pipeline for running kraken2 and bracken in a docker container
  ☆20Updated last month
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 11 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 6 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 9 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• lskatz / lyve-SET
  LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
  ☆27Updated last year
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated last year
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated 2 weeks ago
• BeatsonLab-MicrobialGenomics / micropipe
  A pipeline for high-quality bacterial genome construction using ONT sequencing
  ☆39Updated 3 years ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 7 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆53Updated 4 years ago