Alternatives and similar repositories for pypolca

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

• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆51Updated 2 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆60Updated 2 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆64Updated 5 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆46Updated 2 months ago
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆72Updated last week
• katerinakazantseva / strainy
  Graph-based assembly phasing
  ☆90Updated 6 months ago
• typhoidgenomics / genotyphi
  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
  ☆28Updated 4 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆31Updated last week
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆29Updated last year
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆104Updated 2 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆56Updated 7 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆53Updated 4 years ago
• cmkobel / CompareM2
  🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline
  ☆73Updated last week
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• Ivarz / Conifer
  Calculate confidence scores from Kraken2 output
  ☆23Updated last year
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆33Updated 11 months ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆43Updated 7 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• jlumpe / gambit
  A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
  ☆34Updated 11 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆31Updated 4 months ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆35Updated 6 months ago
• quadram-institute-bioscience / socru
  Order and orientation of complete bacterial genomes
  ☆29Updated 4 months ago
• labgem / PlaScope
  Plasmid exploration of bacterial genomes
  ☆21Updated 3 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• santirdnd / COPLA
  A taxonomic classifier of plasmids
  ☆28Updated 4 years ago
• kwongj / maskrc-svg
  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
  ☆21Updated 6 years ago
• treangenlab / lemur
  Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
  ☆25Updated 3 months ago