bacterial

There are 1 repository under bacterial topic.

• assemblerflow / flowcraft

  FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

  bacterialgenomicsnextflowpipeline
  Language:Python 239

• nf-core / bactmap

  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

  nf-corenextflowworkflowpipelinebacteriabacterialbacterial-genome-analysisphylogenymappinggenomicstree
  Language:Nextflow 49

• quwubin / paired-kmers

  finding conserved regions in highly diverse genomes

  designpcrprimerbacterialkmervirus
  Language:Go 15

• TIBHannover / BacDiveR

  Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.

  rmicroorganismbacterial-databasebacteriologywebservice-clientmicrobiologybiobankr-packagerstatsbacterial-samplesrlangrlanguagebacterialdiversitybacteriaapi-clientbacdive
  Language:R 10

• BV-BRC / BV-BRC-Web

  The BV-BRC Web Application

  bacterialbioinformaticsdojotoolkitgenomicsjavascriptnodejsresource-centerviral
  Language:JavaScript 7

• daniilidisK / TSSextractR

  An R/Shiny Package for Bacterial TSS extraction, using Cappable-seq

  rshinyshiny-rbioconductortssbacterialgenome
  Language:HTML 3
• Computer-vision-in-the-service-of-bacteriology

  NotTheStallion / Computer-vision-in-the-service-of-bacteriology

  Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

  bacteriabacterialbacterial-databasebacterial-genome-analysisbacterial-genomesbashcomputer-visionlearningopencv
  Language:Jupyter Notebook 2

• vrrenske / spotprocessR

  code used in van Raaphorst, Kjos & Veening (2017), Chromosome segregation drives division site selection in Streptococcus pneumoniae, PNAS

  analysis-pipelinebacterialcell-segmentation
  Language:R 2

• chris-c-thomas / BV-BRC-Web

  The BV-BRC Web Application

  bacterialbioinformaticsdojotoolkitgenomicsjavascriptnodejsresource-centerviral
  Language:JavaScript 1

• JFsanchezherrero / BacDup

  Bacterial gene duplication analysis pipeline

  bacterialbioinformatics-pipelinegenomics
  Language:R 1

• AhmedElsherbini / PADLOC_stats

  Condense and summarize many results form PADLOC into CSV for heatmaps

  heatmapsummary-statisticspadlocbacterialbacterial-genomesdefense-systemsdefensome
  Language:Python 0

• MariaDukmak / Staphylococcus-aureus

  Curve Growth modeling-IPASS project

  microbiologystaphylococcus-aureusbacterialgrowth-curve-models
  Language:Python 0

• MaryAgopian / Variant_Barcoding_M.orygis

  Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

  bacterialbacterial-genome-analysisbacterial-genomesbioinformaticsbioinformatics-pipelinegenomic-data-analysisgenomic-data-sciencegenomicsgenomics-visualizationmicrobial-genomesmicrobiologymycobacterium-bovismycobacterium-orygismycobacterium-tuberculosismycobacterium-tuberculosis-complextuberculosis
  Language:R 0

• folkehelseinstituttet / DiscoveryDocker

  Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

  amrbacterialngs-pipelinevirulence
  Language:Python

• garcia-nacho / DiscoveryDocker

  Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

  bacterialngs-pipelineamrvirulence
  Language:Python

• thanhleviet / nextflow-shovill

  🔗 A simple nextflow of shovill for running multiple samples at once on multiple cores computer or HPC (i.e. slurm, sge,...)

  nextflowassemblyshort-readbacterialslurmsingularity