Alternatives and similar repositories for grapevine

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

• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆58Updated 4 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆41Updated last week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆30Updated 9 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆54Updated 3 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆57Updated 4 years ago
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated last year
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆58Updated last year
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated last month
• virus-evolution / gofasta
  ☆36Updated 5 months ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated last month
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• SamStudio8 / reticulatus
  A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
  ☆68Updated 3 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 5 months ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 3 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• rcs333 / VAPiD
  VAPiD: Viral Annotation and Identification Pipeline
  ☆54Updated last year
• bobeobibo / phigaro
  Phigaro is a scalable command-line tool for predicting phages and prophages
  ☆52Updated last year
• will-rowe / groot
  A resistome profiler for Graphing Resistance Out Of meTagenomes
  ☆65Updated 5 years ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆45Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆66Updated 3 years ago