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algorithmvisualizationd3

Graph algorithms and other algorithms described with cool interactive visualizations

anopheles_popgen_graphref

assembly_comparison_scripts

astar-pairwise-aligner

A pairwise sequence aligner written in Rust

bigly

a pileup library that embraces the huge

blokus

Learning golang through project creating a simple AI and visualization for the board game blokus

clustering_visualization

implementations and visualizations of several clustering algorithms. For private fun and maybe for teaching purposes

comp5970

complete-striped-smith-waterman-library

configfiles

deep_filter_clustering

discreteoptimization

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

ensemblign

Bayesian multiple sequence alignment using forward/backward HMM pairwise alignments and a novel Kargers algorithm based multiple alignment.

fastk

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

graphalgorithmsviz

GraphAlgorithmsViz

graphcoloring

haplossembly

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

hts

biogo high throughput sequencing repository

long_read_binner

tool to bin long noisy DNA reads by kmer sets

martian

Language and framework for high performance computational pipelines.

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

pedigree_data_simulator

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

phaser

it phases

phasst

Phased Assembly Tool