Alternatives and similar repositories for scrubby:

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

• iqbal-lab-org / cobs
  COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
  ☆19Updated 5 months ago
• oxli-bio / oxli
  k-mers and the like
  ☆21Updated this week
• bluenote-1577 / devider
  Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs
  ☆20Updated 5 months ago
• mbhall88 / psdm
  Compute a pairwise SNP distance matrix from one or two alignment(s)
  ☆25Updated 7 months ago
• esteinig / brick
  BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons
  ☆17Updated last month
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 3 months ago
• hcdenbakker / colorid
  Experiments with using BIGSI data structure for metagenomic and QC applications
  ☆19Updated 8 months ago
• rust-seq / minimizer-iter
  Iterate over minimizers of a DNA sequence
  ☆28Updated 9 months ago
• St4NNi / jam-rs
  Just another minhash implementation.
  ☆12Updated last month
• tongzhouxu / mashpit
  Sketch-based surveillance platform
  ☆13Updated 4 months ago
• mbhall88 / drprg
  Drug Resistance Prediction with Reference Graphs
  ☆20Updated last year
• Malfoy / NIQKI
  Next Index to Query Kmer Intersection
  ☆16Updated 2 years ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 months ago
• mbhall88 / skc
  Shared k-mer content between two genomes
  ☆17Updated last year
• moold / kseq-rs
  A FASTA/FASTQ format parser library
  ☆20Updated last year
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated last year
• kangxiongbin / HyLight
  HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…
  ☆10Updated 7 months ago
• fpusan / SuperPang
  Non-redundant pangenome assemblies from multiple genomes or bins
  ☆13Updated 2 months ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 2 months ago
• natir / rustyread
  A long read simulator based on badread idea
  ☆22Updated 2 years ago
• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated 11 months ago
• KoslickiLab / YACHT
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome
  ☆30Updated 2 weeks ago
• bo1929 / krepp
  A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.
  ☆10Updated this week
• sourmash-bio / sourmash_plugin_branchwater
  fast, multithreaded sourmash operations: search, compare, and gather.
  ☆22Updated this week
• Kalan-Lab / codoff
  codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the fu…
  ☆11Updated 3 weeks ago
• unipept / umgap
  A taxonomic classifier for shotgun metagenomics reads
  ☆12Updated 3 weeks ago
• algbio / matchtigs
  Minimum plain text representation of kmer sets
  ☆17Updated 2 months ago
• RagnarGrootKoerkamp / simd-sketch
  Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
  ☆16Updated last month
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆27Updated last week
• pg-space / panspace
  Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
  ☆10Updated last week