Alternatives and similar repositories for StrainGE

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

• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆52Updated 4 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆56Updated 7 months ago
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• ikmb / MAGScoT
  MAGScoT - a MAG scoring and refinement tool
  ☆37Updated last year
• pollardlab / MIDAS
  Metagenomic Intra-Species Diversity Analysis (MIDAS)
  ☆39Updated last year
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆53Updated last month
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 11 months ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated last week
• lmlui / Jorg
  MAG Circularization Method
  ☆32Updated 2 weeks ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆25Updated last year
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆31Updated 3 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆50Updated 3 years ago
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated last month
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 6 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆43Updated 5 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 8 months ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last month
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆29Updated 8 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆31Updated last month
• AlexanderLabWHOI / EUKulele
  Automatic eukaryotic taxonomic classification
  ☆28Updated 6 months ago
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆14Updated 3 years ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 2 years ago