wheaton5
Assistant professor at Auburn University CSSE department. Rustacean, Gopher, and pythonista
Auburn University CSSEAuburn, AL
Pinned Repositories
Complete-Striped-Smith-Waterman-Library
distinguishing_kmers
Memory efficient (approximate) thresholded kmer set subtraction using mod hash minimizer.
dna_io
automatic reading of fastq, fastq.gz, fasta, and possibly sam and bam (and cram?) and writing to your choice of format
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
long_read_binner
tool to bin long noisy DNA reads by kmer sets
pedigree_data_simulator
Python scripts for simulating pedigree haplotypes and short and long reads from those haplotypes.
phasstools
phasing and assembly tools
souporcell
Clustering scRNAseq by genotypes
wheaton5's Repositories
wheaton5/souporcell
Clustering scRNAseq by genotypes
wheaton5/long_read_binner
tool to bin long noisy DNA reads by kmer sets
wheaton5/phasstools
phasing and assembly tools
wheaton5/distinguishing_kmers
Memory efficient (approximate) thresholded kmer set subtraction using mod hash minimizer.
wheaton5/haplovalidate
method for validating genome assemblies using heterozygous kmers detected from short read data
wheaton5/het_snp_kmers
het snp detection from sorted kmc kmer database dump
wheaton5/het_snp_kmers2
wheaton5/pedigree_data_simulator
Python scripts for simulating pedigree haplotypes and short and long reads from those haplotypes.
wheaton5/dna_io
automatic reading of fastq, fastq.gz, fasta, and possibly sam and bam (and cram?) and writing to your choice of format
wheaton5/intro_algorithms
course material for introduction to algorithms course at auburn university I am teaching
wheaton5/phasst_lib
library for shared code in phasing and assembly tools projects
wheaton5/cellector
statistical model for finding anomalous genotype cells in mixed genotype scRNAseq data
wheaton5/GraphAlgorithmsViz
GraphAlgorithmsViz
wheaton5/assembly_comparison_scripts
wheaton5/astar-pairwise-aligner
A pairwise sequence aligner written in Rust
wheaton5/comp5970
wheaton5/deep_filter_clustering
wheaton5/FASTK
A fast K-mer counter for high-fidelity shotgun datasets
wheaton5/mixhap
Using either sparse mixture model clustering or sparse fuzzy kmeans as a method of haplotype phasing 10x linked reads or Hi-C data
wheaton5/molecule_kmers
Find kmers of interest on long reads, linked reads, and HiC data
wheaton5/phaser
it phases
wheaton5/phasst
Phased Assembly Tool
wheaton5/phasst_break
wheaton5/phasst_phase
Sparse mixture model diploid and polyploid phasing
wheaton5/phasst_scaff
Phased Assembly Tool Scaffolder
wheaton5/phd_thesis
wheaton5/phuzzyphase
wheaton5/poa_test
wheaton5/vcf_compare
scripts to compare vcf files
wheaton5/wheaton5.github.io