Alternatives and similar repositories for pango-sequences:

Users that are interested in pango-sequences are comparing it to the libraries listed below

• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆22Updated 2 months ago
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆51Updated this week
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆73Updated this week
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆34Updated 4 months ago
• Kalan-Lab / lsaBGC
  lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
  ☆37Updated 5 months ago
• bede / hostile
  Precise host read removal
  ☆84Updated 3 weeks ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆32Updated last month
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆22Updated last year
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 6 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆56Updated last year
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆33Updated this week
• virus-evolution / gofasta
  ☆35Updated 5 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆28Updated 6 months ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆29Updated last year
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆30Updated last month
• CCB-SB / plsdb
  PLSDB pipeline to collect bacterial plasmids from NCBI
  ☆37Updated 2 months ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆94Updated this week
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆29Updated this week
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆46Updated 2 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆49Updated last month
• pha4ge / hAMRonization_workflow
  Harmonization of AMR predictor tool outputs
  ☆22Updated this week
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆34Updated last month
• iqbal-lab-org / viridian
  ☆16Updated this week
• nextstrain / avian-flu
  Nextstrain build for avian influenza viruses
  ☆22Updated this week
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 3 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆87Updated this week
• simonrharris / SKA
  Split Kmer Analysis
  ☆63Updated 2 years ago
• susiegriggo / Phynteny
  Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
  ☆43Updated last month
• klebgenomics / Kaptive
  ☆44Updated this week