jeizenga

wfalm

Refinements of the WFA alignment algorithm with better complexity

centrolign

Multiple sequence alignment of long tandem repeats

SeqPrep2

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

structures

A collection of c++ data structures I've coded up for various projects

dissertation

hdp_mixture

Hierarchical Dirichlet process mixture model

handle_eval

reproduce_vg_results

vg

tools for working with variation graphs

cwl-intro-gui-workshop

Materials to teach workshop about CWL using the Rabix Composer

alphaAnnotation

gbwt

Substring index for paths in a graph

gbwtgraph

GBWT-based handle graph

gcsa2

BWT-based index for graphs

genome-stratifications

Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium. These files can be used as standard resource of BED files for use with GA4GH benchmarking tools such as hap.py to stratify true positive, false positive, and false negative variant calls based on genomic context.

gssw

efficient alignment of strings to partially ordered string graphs

mmmultimap

memory mapped multimap based on an in-place parallel binary sort and succinct indexes

mummer

Mummer alignment tool

odgi

optimized dynamic genome graph implementation

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

rpvg

Method for inferring path posterior probabilities and abundances from pangenome graph read alignments

scikit-learn

scikit-learn: machine learning in Python

sglib

Optimized sequence graph implementations for graph genomics

shasta

Experimental software for de novo assembly from Nanopore sequencing data.

Ukkonen-SuffixTree

A C++ implementation of a Generalized Suffix Tree using Ukkonen's algorithm

VerityMap

vgrna-project-scripts

Scripts used in vgrna project

whatshap

Read-based phasing of genomic variants, also called haplotype assembly

xg

succinct labeled graphs with collections and paths

xg-1

xg0: a simpler xg index