Alternatives and similar repositories for pykofamsearch

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

• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆28Updated 4 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 9 months ago
• KatyBrown / plot_phylo
  Python package to plot a phylogenetic tree on an existing matplotlib axis.
  ☆27Updated 5 months ago
• cruizperez / FastAAI
  ☆24Updated 11 months ago
• althonos / pysylph
  PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
  ☆20Updated last year
• NickJD / ORForise
  Comparison pipeline for Prokaryote Protein Coding Gene Predictors
  ☆28Updated last week
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated 2 years ago
• moshi4 / pybarrnap
  Python implementation of barrnap (Bacterial ribosomal RNA predictor)
  ☆23Updated 11 months ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆49Updated 4 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆52Updated 4 years ago
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆44Updated 9 months ago
• bluenote-1577 / fairy
  alignment-free coverage calculation for metagenomic binning >100 times faster
  ☆48Updated 10 months ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆39Updated last year
• zjshi / Maast
  Microbial agile accurate SNP Typer
  ☆30Updated 2 years ago
• unipept / FragGeneScanRs
  Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.
  ☆30Updated 3 months ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆33Updated 5 months ago
• rrwick / Are-reads-required
  ☆10Updated 7 months ago
• jlumpe / gambit
  A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
  ☆35Updated last year
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated last week
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated 2 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆80Updated last month
• bioinf-mcb / MANIAC
  Computation of average nucleotide identity with the use of MMseqs2
  ☆15Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 4 months ago
• ku-cbd / PhageBoost
  Rapid discovery of novel prophages using biological feature engineering and machine learning
  ☆36Updated last year
• SegataLab / viromeqc
  ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichmen…
  ☆20Updated 3 years ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆47Updated last month
• Kalan-Lab / codoff
  codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, prophage, etc.) relative to the…
  ☆13Updated this week
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆24Updated 2 years ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆22Updated 5 months ago
• althonos / pyrodigal-gv
  A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
  ☆20Updated last month