jeizenga
Postdoc in the Computational Genomics Lab at UCSC working on a variety of topics in and around pangenomics
University of California Santa Cruz Genomics InstituteLos Angeles, CA
Pinned Repositories
centrolign
Multiple sequence alignment of long tandem repeats
dissertation
handle_eval
hdp_mixture
Hierarchical Dirichlet process mixture model
reproduce_vg_results
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
vg
tools for working with variation graphs
wfalm
Refinements of the WFA alignment algorithm with better complexity
libbdsg
Optimized sequence graph implementations for graph genomics
jeizenga's Repositories
jeizenga/wfalm
Refinements of the WFA alignment algorithm with better complexity
jeizenga/centrolign
Multiple sequence alignment of long tandem repeats
jeizenga/SeqPrep2
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
jeizenga/structures
A collection of c++ data structures I've coded up for various projects
jeizenga/dissertation
jeizenga/hdp_mixture
Hierarchical Dirichlet process mixture model
jeizenga/handle_eval
jeizenga/reproduce_vg_results
jeizenga/vg
tools for working with variation graphs
jeizenga/cwl-intro-gui-workshop
Materials to teach workshop about CWL using the Rabix Composer
jeizenga/alphaAnnotation
jeizenga/gbwt
Substring index for paths in a graph
jeizenga/gbwtgraph
GBWT-based handle graph
jeizenga/gcsa2
BWT-based index for graphs
jeizenga/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.
jeizenga/gssw
efficient alignment of strings to partially ordered string graphs
jeizenga/mmmultimap
memory mapped multimap based on an in-place parallel binary sort and succinct indexes
jeizenga/mummer
Mummer alignment tool
jeizenga/odgi
optimized dynamic genome graph implementation
jeizenga/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.
jeizenga/rpvg
Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
jeizenga/scikit-learn
scikit-learn: machine learning in Python
jeizenga/sglib
Optimized sequence graph implementations for graph genomics
jeizenga/shasta
Experimental software for de novo assembly from Nanopore sequencing data.
jeizenga/Ukkonen-SuffixTree
A C++ implementation of a Generalized Suffix Tree using Ukkonen's algorithm
jeizenga/VerityMap
jeizenga/vgrna-project-scripts
Scripts used in vgrna project
jeizenga/whatshap
Read-based phasing of genomic variants, also called haplotype assembly
jeizenga/xg
succinct labeled graphs with collections and paths
jeizenga/xg-1
xg0: a simpler xg index