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
  ☆60Updated last year
• 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 7 months ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆124Updated 3 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆86Updated 3 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆79Updated last week
• apcamargo / taxopy
  A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
  ☆52Updated last week
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years 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
• linsalrob / SRA_Metadata
  Get, parse, and extract information from the SRA metadata files
  ☆45Updated 3 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• iquasere / KEGGCharter
  A tool for representing genomic potential and transcriptomic expression into KEGG pathways
  ☆60Updated last year
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆56Updated this week
• EBI-Metagenomics / mettannotator
  ☆80Updated last week
• gatech-genemark / ProtHint
  Protein hint generation pipeline for gene finding in eukaryotic genomes
  ☆60Updated 2 years ago
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated last year
• art-egorov / lovis4u
  Bioinformatics tool for Locus Visualisation
  ☆143Updated last month
• widdowquinn / find_differential_primers
  Code for design of diagnostic PCR primers, and metabarcoding markers.
  ☆63Updated 2 years ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• mourisl / Rcorrector
  Error correction for Illumina RNA-seq reads
  ☆67Updated last year
• refresh-bio / vclust
  Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
  ☆92Updated 6 months ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 5 months ago
• pauloluniyi / VGEA
  VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
  ☆20Updated 4 years ago
• JustineCharon / RdRp-scan
  Exploring the "dusk matter" of the RNA virosphere
  ☆35Updated 3 years ago
• replikation / poreCov
  SARS-CoV-2 workflow for nanopore sequence data
  ☆42Updated 3 months ago
• DessimozLab / FastOMA
  FastOMA is a scalable software package to infer orthology relationship.
  ☆84Updated last week
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆72Updated 4 years ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆71Updated 3 years ago