bluenote-1577

skani

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

flopp

flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.

floria

Strain-level haplotyping for metagenomes with short or long-reads.

fairy

alignment-free coverage calculation for metagenomic binning >100 times faster

os-minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

sce-aligner

A basic seed-chain-extend aligner with linear-gap cost chaining and quadratic time extension for experiments

sylph-utils

Utility scripts and helpers for sylph

basic_seed_chainer

ANI

Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes

local-kmer-selection-results

partitions

A disjoint-sets/union-find implementation that allows for efficient iteration over the elements of a set.

plume

skani-test

sylph-test

bay

🐟 A simple theme for Jekyll. Live at https://eliottvincent.github.io/bay/

bioconda-recipes

Conda recipes for the bioconda channel.

chrom_mini_graph

fairy-test

Scripts for benchmarking fairy

flopp_test

Testing pipeline for flopp paper.

highs-sys

Rust binding for the HiGHS linear programming solver

markdown_readme

Markdown - you can mark up titles, lists, tables, etc., in a much cleaner, readable and accurate way if you do it with HTML.

meta-cmg

nthash

ntHash implementation in Rust

phase-doc

Template for the Read the Docs tutorial

rs-liftover

Simple sequence mapping liftover tool

rs-wfa

Rust bindings to the wavefront algorithm C implementation

skani-lib-example

Example for how to use skani as a rust library.

skani-mummer-train

Repository for training skani on mummer data to improve accuracy.

vartig-utils