Alternatives and similar repositories for sc2rf

Users that are interested in sc2rf are comparing it to the libraries listed below

• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆36Updated this week
• corneliusroemer / pango_aliasor
  Utility to alias and dealias pango lineages
  ☆23Updated last year
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 3 months ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated this week
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆91Updated last month
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last month
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆31Updated last week
• CFSAN-Biostatistics / C-WAP
  SC2 variant detection and composition pipeline
  ☆17Updated 2 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆37Updated 3 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 3 weeks ago
• oschwengers / referenceseeker
  Rapid determination of appropriate reference genomes.
  ☆97Updated 8 months ago
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆57Updated last year
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆57Updated this week
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆29Updated last year
• phac-nml / rebar
  REcombination BARcode detector.
  ☆16Updated last year
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated 11 months ago
• sdellicour / seraphim
  R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al., in prep.)
  ☆34Updated 3 weeks ago
• virus-evolution / gofasta
  ☆36Updated 5 months ago
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 3 years ago
• DOH-JDJ0303 / bigbacter-nf
  Bacterial surveillance pipeline.
  ☆26Updated 3 months ago
• AMRverse / AMRrules
  Interpretative standards for AMR genotypes
  ☆25Updated this week
• DOH-JDJ0303 / vaper
  Viral (meta)-genome assembly pipeline.
  ☆17Updated 3 weeks ago
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆29Updated 2 years ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated last year
• andersen-lab / Freyja
  Depth-weighted De-Mixing
  ☆119Updated this week
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 3 years ago
• richardmleggett / MARTi
  Metagenomic Analysis in Real Time
  ☆28Updated this week
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago