Alternatives and similar repositories for genepi-book

Users that are interested in genepi-book are comparing it to the libraries listed below

• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆47Updated this week
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆87Updated last week
• bede / hostile
  Precise host read removal
  ☆108Updated 2 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated 8 months ago
• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated 2 years ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆59Updated 3 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆129Updated 3 months ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated 2 years ago
• andersen-lab / Freyja
  Depth-weighted De-Mixing
  ☆125Updated last week
• artic-network / fieldbioinformatics
  The ARTIC fieldbioinformatics pipeline
  ☆126Updated last month
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆38Updated 3 weeks ago
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆57Updated this week
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆92Updated 3 months ago
• jodyphelan / tbdb
  Standard database for the TBProfiler tool
  ☆31Updated 3 months ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆144Updated 3 months ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated last month
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated 2 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated last month
• virus-evolution / gofasta
  ☆36Updated 7 months ago
• boulund / phaster_scripts
  Small utility script to submit genomes to PHASTER for phage detection
  ☆24Updated 4 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆50Updated last year
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆40Updated last month
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆124Updated 3 months ago
• jolespin / veba
  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metag…
  ☆96Updated last month
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆81Updated last month
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 3 months ago
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆39Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆42Updated last month
• voorloopnul / awesome-phages
  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
  ☆50Updated 3 years ago