Name: Erik Garrison
Type: User
Company: University of Tennessee Health Science Center (UTHSC)
Bio: Assistant professor at the University of Tennessee Health Science Center / bioinformatician / sequence analysis and pangenomes
Twitter: erikgarrison
Location: Memphis, TN / Lavello, IT
Blog: http://hypervolu.me/~erik/erik_garrison.html
Erik Garrison's Projects
tools for manipulating tab-separated-values files, mostly in C++
A fast constructor of the compressed de Bruijn graph from many genomes
determines if the primers required to assay VCF records are unique (provided BAM alignments of the primers and a VCF file of the variants)
assists in importing the USDA's SR22 nutritional database from MS Access to MySQL
extensions for manipulating VCF files annotated with the Variant Annotation Tool (VAT)
Database that replicates based on scuttlebutt logs and causal linking
exploring viral genome assembly with variation graph tools
Portable file system cache diagnostics and control
Vowpal Wabbit is a machine learning system which pushes the frontier of machine learning with techniques such as online, hashing, allreduce, reductions, learning2search, active, and interactive learning.
variant quality recalibration by artificial neural network
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
WFλ - wavefront alignment with callback match function
the we-flyin WFA-guided ultralong tiling sequence aligner
All-things-BAM
an xml to .tsv converter for wikimedia XML data dumps
XBzip/XBWT implementation from "Compressing and indexing labeled trees, with applications," P Ferragina et al.
A C++ Library that defines a templated XOR-Linked List
yeast pangenome
A small shell like bash with pure C++, based on flex, bison and readline.