wheaton5

souporcell

Clustering scRNAseq by genotypes

long_read_binner

tool to bin long noisy DNA reads by kmer sets

phasstools

phasing and assembly tools

distinguishing_kmers

Memory efficient (approximate) thresholded kmer set subtraction using mod hash minimizer.

haplovalidate

method for validating genome assemblies using heterozygous kmers detected from short read data

het_snp_kmers

het snp detection from sorted kmc kmer database dump

het_snp_kmers2

pedigree_data_simulator

Python scripts for simulating pedigree haplotypes and short and long reads from those haplotypes.

dna_io

automatic reading of fastq, fastq.gz, fasta, and possibly sam and bam (and cram?) and writing to your choice of format

intro_algorithms

course material for introduction to algorithms course at auburn university I am teaching

phasst_lib

library for shared code in phasing and assembly tools projects

cellector

statistical model for finding anomalous genotype cells in mixed genotype scRNAseq data

GraphAlgorithmsViz

GraphAlgorithmsViz

assembly_comparison_scripts

astar-pairwise-aligner

A pairwise sequence aligner written in Rust

comp5970

deep_filter_clustering

FASTK

A fast K-mer counter for high-fidelity shotgun datasets

mixhap

Using either sparse mixture model clustering or sparse fuzzy kmeans as a method of haplotype phasing 10x linked reads or Hi-C data

molecule_kmers

Find kmers of interest on long reads, linked reads, and HiC data

phaser

it phases

phasst

Phased Assembly Tool

phasst_break

phasst_phase

Sparse mixture model diploid and polyploid phasing

phasst_scaff

Phased Assembly Tool Scaffolder

phd_thesis

phuzzyphase

poa_test

vcf_compare

scripts to compare vcf files

wheaton5.github.io