Jim Shaw

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

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

myloasm. A new high-resolution long-read metagenome assembler for even noisy reads

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

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

savont. Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads

devider. Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs

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

sylph-tax. Taxonomy manipulation for sylph (new version)

os-minimap2. A versatile pairwise aligner for genomic and spliced nucleotide sequences

sylph-test. HTML

rust-anvio-mis. A rust reimplementation of a script for finding local metagenomic misassemblies

sylph-utils. Utility scripts and helpers for sylph

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

dbghaplo. Long-read haplotyping of small sequences with SNP-encoded de Bruijn graphs

mylotools. Utility scripts for the myloasm long-read metagenomic assembler.

basic_seed_chainer. Rust

plume. Rust

local-kmer-selection-results. Jupyter Notebook

ttk. TTK - Topological Data Analysis and Visualization - Source Code

ANI. Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes

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

skani-test. Jupyter Notebook