Alternatives and similar repositories for avian-flu

Users that are interested in avian-flu are comparing it to the libraries listed below

• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 2 months ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated last month
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆16Updated 7 months ago
• cmmr / EsViritu
  Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
  ☆48Updated 2 weeks ago
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆47Updated this week
• theiagen / public_health_bioinformatics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…
  ☆58Updated this week
• iqtree / piqtree
  A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference
  ☆38Updated last week
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated last month
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆60Updated last year
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆44Updated 4 months ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆60Updated 2 weeks ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆48Updated last week
• virus-evolution / gofasta
  ☆36Updated 8 months ago
• 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
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 7 months ago
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆27Updated 2 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆39Updated last week
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆96Updated 2 months ago
• vinisalazar / metaphor
  Metaphor: a general-purpose workflow for assembly and binning of metagenomes
  ☆40Updated last month
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆25Updated 2 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆54Updated last month
• refresh-bio / vclust
  Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
  ☆95Updated 6 months ago
• peterk87 / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆31Updated 2 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 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 last year
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆101Updated 2 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆62Updated 3 months ago
• NicolaDM / MAPLE
  MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.
  ☆57Updated last month
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 5 months ago
• dib-lab / genome-grist
  map Illumina metagenomes to genomes!
  ☆38Updated this week