Alternatives and similar repositories for strainberry

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

• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆62Updated 8 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• rrwick / Verticall
  Recombination-free trees
  ☆62Updated 3 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆49Updated 3 months ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 3 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 6 months ago
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆113Updated this week
• Arkadiy-Garber / SprayNPray
  Rapid and simple taxonomic profiling of genome and metagenome contigs
  ☆29Updated 2 years ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆31Updated 5 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 5 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆66Updated 3 years ago
• ChrispinChaguza / RCandy
  RCandy: an R package for visualising homologous recombination events in bacterial genomes
  ☆25Updated 3 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated last month
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆32Updated 2 weeks ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated 3 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 7 months ago
• Dmitry-Antipov / viralFlye
  viralFlye pipeline
  ☆18Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆34Updated last year
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• Sudaraka88 / LDWeaver
  Genomewide Epistasis Analysis on Bacteria
  ☆15Updated 7 months ago
• cruizperez / FastAAI
  ☆24Updated 10 months ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 8 months ago
• wanyuac / GeneMates
  An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
  ☆27Updated 3 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆39Updated last year