Alternatives and similar repositories for mandrake

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

• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆55Updated 5 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated last month
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆61Updated 2 weeks ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 3 years ago
• santeripuranen / SpydrPick
  SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
  ☆13Updated 3 years ago
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 7 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆50Updated 3 years ago
• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• bacpop / CELEBRIMBOR
  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
  ☆25Updated last year
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆39Updated 2 weeks ago
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆39Updated 11 months ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆47Updated 2 years ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated 2 months ago
• josephpetrone / RESCUE
  Resolving Species Level Classification Using Emu
  ☆14Updated last year
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated last month
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆22Updated 2 years ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated last year
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 6 months ago
• lmlui / Jorg
  MAG Circularization Method
  ☆32Updated 3 years ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 2 months ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆26Updated 3 years ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated last week