Alternatives and similar repositories for czid-workflows:

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

• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 7 months ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• art-egorov / lovis4u
  Bioinformatics tool for Locus Visualisation
  ☆101Updated last month
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆108Updated 5 months ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆97Updated this week
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 4 months ago
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆57Updated 3 weeks ago
• nf-core / pangenome
  Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
  ☆88Updated 2 months ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 3 weeks ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• jodyphelan / tbdb
  Standard database for the TBProfiler tool
  ☆29Updated last month
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆121Updated last year
• mourisl / Rcorrector
  Error correction for Illumina RNA-seq reads
  ☆66Updated last year
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆49Updated this week
• sanger-pathogens / pathogen-informatics-training
  ☆69Updated 4 years ago
• nadegeguiglielmoni / genome_assembly_tools
  List of genome assembly tools
  ☆65Updated 3 weeks ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• apcamargo / taxopy
  A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
  ☆48Updated 2 months ago
• EBI-Metagenomics / mettannotator
  ☆69Updated last month
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆76Updated this week
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆26Updated 2 weeks ago
• jolespin / veba
  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metag…
  ☆83Updated last week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆79Updated last year
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆36Updated 2 months ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆57Updated 3 weeks ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• ngs-fzb / MTBseq_source
  MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…
  ☆44Updated 8 months ago
• genotoul-bioinfo / dgenies
  Dotplot large Genomes in an Interactive, Efficient and Simple way
  ☆103Updated 3 months ago
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆91Updated last month
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆57Updated 7 months ago