Name: Jordan Eizenga
Type: User
Company: University of California Santa Cruz Genomics Institute
Bio: Postdoc in the Computational Genomics Lab at UCSC working on a variety of topics in and around computational pangenomics
Twitter: jeizenga
Location: Los Angeles, CA
Blog: https://scholar.google.com/citations?user=rWNHPpAAAAAJ&hl=en&oi=ao
Jordan Eizenga's Projects
Multiple sequence alignment of long tandem repeats
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
Materials to teach workshop about CWL using the Rabix Composer
Substring index for paths in a graph
GBWT-based handle graph
BWT-based index for graphs
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.
efficient alignment of strings to partially ordered string graphs
Hierarchical Dirichlet process mixture model
memory mapped multimap based on an in-place parallel binary sort and succinct indexes
Mummer alignment tool
optimized dynamic genome graph implementation
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.
Repository for Programming Assignment 2 for R Programming on Coursera
Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
scikit-learn: machine learning in Python
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
Optimized sequence graph implementations for graph genomics
Experimental software for de novo assembly from Nanopore sequencing data.
A collection of c++ data structures I've coded up for various projects
A C++ implementation of a Generalized Suffix Tree using Ukkonen's algorithm
tools for working with variation graphs
Scripts used in vgrna project
Refinements of the WFA alignment algorithm with better complexity