Alternatives and similar repositories for bonsai:

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

• will-rowe / hulk
  Histosketching Using Little Kmers
  ☆55Updated last year
• shenwei356 / strobemers
  A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)
  ☆14Updated 3 years ago
• splatlab / squeakr
  Squeakr: An Exact and Approximate k -mer Counting System
  ☆85Updated 11 months ago
• COMBINE-lab / kmers
  A bit-packed k-mer representation (and relevant utilities) for rust
  ☆47Updated 6 months ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• edawson / rkmh
  Classify sequencing reads using MinHash.
  ☆48Updated 4 years ago
• benedictpaten / sonLib
  Small general purpose library for C and Python with focus on bioinformatics.
  ☆29Updated 2 years ago
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆64Updated last month
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆44Updated 2 years ago
• VGP / vgp-tools
  ☆28Updated last year
• natir / yacrd
  Yet Another Chimeric Read Detector
  ☆73Updated 2 months ago
• johanneskoester / alpaca
  ALPACA is a caller for genomic variants (single nucleotide and small indels) from next-generation sequencing data that uses a novel algeb…
  ☆23Updated last month
• edawson / mkmh
  Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
  ☆24Updated 4 years ago
• cosmo-team / cosmo
  Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
  ☆51Updated 10 months ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆34Updated last year
• arshajii / ema
  Fast & accurate alignment of barcoded short-reads
  ☆33Updated last year
• lskatz / fasten
  Fasten toolkit, for streaming operations on fastq files
  ☆77Updated this week
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 5 years ago
• bcgsc / ntCard
  Estimating k-mer coverage histogram of genomics data
  ☆76Updated last year
• ddiazdom / lcg
  Efficient, parallel compression for terabyte-scale data
  ☆36Updated this week
• hcdenbakker / colorid
  Experiments with using BIGSI data structure for metagenomic and QC applications
  ☆18Updated 5 months ago
• ekg / viral-assembly
  exploring viral genome assembly with variation graph tools
  ☆19Updated 4 years ago
• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• bcgsc / ntLink
  Minimizer-based assembly scaffolding and mapping using long reads
  ☆34Updated 3 months ago
• rvaser / rala
  Layout module for raw de novo genome assembly of long uncorrected reads.
  ☆21Updated 3 years ago
• NBISweden / pipelines-nextflow
  A set of workflows written in Nextflow for Genome Annotation.
  ☆44Updated 6 months ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated 5 months ago
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆52Updated 2 months ago
• ksahlin / strobemers
  A repository for generating strobemers and evalaution
  ☆77Updated 9 months ago
• natir / fpa
  Filter of Pairwise Alignement
  ☆44Updated 2 years ago