Alternatives and similar repositories for CaveDive:

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

• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 2 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆37Updated last week
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆36Updated last month
• andersgs / harrietr
  An `R` package for various phylogenetic and evolutionary biology data manipulations
  ☆12Updated 7 years ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated last week
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆18Updated 6 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated last week
• martinghunt / tna
  ☆14Updated 2 weeks ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆18Updated 4 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 9 months ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆12Updated 10 months ago
• phac-nml / rebar
  REcombination BARcode detector.
  ☆13Updated last year
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 3 months ago
• CFSAN-Biostatistics / shigatyper
  CFSAN Shigella Typing Pipeline
  ☆14Updated last year
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆29Updated 3 weeks ago
• stjacqrm / centroid
  tool to determine optimal refrerence genome given a set of fasta files
  ☆14Updated last year
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆28Updated last year
• CFIA-NCFAD / nf-flu
  Influenza genome analysis Nextflow workflow
  ☆22Updated 2 weeks ago
• niemasd / ViralConsensus
  Fast viral consensus genome reconstruction
  ☆22Updated 4 months ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 6 months ago
• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆15Updated 2 years ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 9 months ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆36Updated 6 months ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• gbouras13 / pypolca
  Standalone Python re-implementation of the POLCA polisher from MaSuRCA
  ☆34Updated last month