Alternatives and similar repositories for public_health_bioinformatics

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

• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 8 months ago
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated last year
• simonrharris / SKA
  Split Kmer Analysis
  ☆64Updated 2 years ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated 9 months ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆44Updated 4 years ago
• bede / hostile
  Precise host read removal
  ☆94Updated 3 weeks ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 4 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆40Updated 5 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 8 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆42Updated last month
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆57Updated 3 weeks ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆40Updated 3 years ago
• jodyphelan / tbdb
  Standard database for the TBProfiler tool
  ☆29Updated 2 months ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated 3 weeks ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆102Updated 3 weeks ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆97Updated last month
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆117Updated last month
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆27Updated 3 weeks ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆48Updated last year
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆49Updated last year
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆37Updated 2 months ago
• denglab / SeqSero2
  SeqSero2
  ☆35Updated last year
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 2 months ago
• paulstothard / cgview
  CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
  ☆44Updated 10 months ago