Alternatives and similar repositories for czid-workflows

Users that are interested in czid-workflows are comparing it to the libraries listed below

• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 8 months ago
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆87Updated 2 years ago
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆59Updated this week
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆99Updated last week
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆63Updated 6 months ago
• MicrobeLab / DeepMicrobes
  DeepMicrobes: taxonomic classification for metagenomics with deep learning
  ☆102Updated 3 years ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆127Updated 4 months ago
• broadinstitute / viral-pipelines
  viral-ngs: complete pipelines
  ☆70Updated this week
• linsalrob / SRA_Metadata
  Get, parse, and extract information from the SRA metadata files
  ☆45Updated 3 years ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆72Updated 4 years ago
• BenLangmead / aws-indexes
  Catalog of genomic indexes freely available from public clouds
  ☆65Updated 2 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆88Updated 3 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• metagenlab / MeSS
  Snakemake pipeline for simulating shotgun metagenomic samples
  ☆28Updated 4 months ago
• paulstothard / cgview
  CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
  ☆50Updated last year
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆72Updated 3 years ago
• qiyunzhu / woltka
  Woltka: a versatile meta'omic data classifier
  ☆76Updated 4 months ago
• telatin / seqfu2
  seqfu - Sequece Fastx Utilities
  ☆124Updated 2 weeks ago
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆31Updated 3 months ago
• happykhan / BRIG
  BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a f…
  ☆37Updated 6 years ago
• widdowquinn / find_differential_primers
  Code for design of diagnostic PCR primers, and metabarcoding markers.
  ☆62Updated 2 years ago
• ohmeta / metapi
  A general metagenomics data mining system focus on robust microbiome research
  ☆58Updated last year
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆97Updated last month
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆80Updated last month
• sanger-pathogens / pathogen-informatics-training
  ☆75Updated 5 years ago