Erik Garrison

intervaltree. a minimal C++ interval tree implementation

alignment-and-variant-calling-tutorial. basic walk-throughs for alignment and variant calling from NGS sequencing data

fraction.js. A fraction math library in javascript.

fastahack. utilities for indexing and sequence extraction from FASTA files

bamaddrg. adds sample names and read-group (RG) tags to BAM alignments

glia. a string to graph aligner

thesis. my PhD thesis

pafplot. base-level dotplots from PAF alignments

edyeet. base-accurate DNA sequence alignments using edlib and mashmap2

mmmulti. memory mapped multimap, multiset, and implicit interval tree based on an in-place parallel sort

split. split and join for C++ strings

multichoose. generate multiset combinations (n multichoose k)

gimbricate. recompute GFA link overlaps

HLA-zoo. genome variation graphs constructed from HLA GRCh38 ALTs

guix-genomics. guix packages for bioinformatics software

multipermute. efficient multiset permutations

1000G-integration. variant integration methods for the 1000 Genomes Project

viral-assembly. exploring viral genome assembly with variation graph tools

openconnect-sso-docker. connect to a cisco anyconnect server with 2FA via web SSO on a headless server

hhga. haplotypes genotypes and alleles example decision synthesizer

shuntingyard. implementations of Dijkstra's shunting-yard algorithm for infix notation parsing

ogap. gap opening realigner for BAM data streams

smithwaterman. smith-waterman-gotoh alignment algorithm

fastix. Prefix-renaming FASTA records really fast.

drawbwt. vector illustrations of BWT based searching on small strings

mutatrix. genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms

pafcheck. PAF (pairwise alignment format) validator based on extended CIGAR strings

USDA-SR22-importer. assists in importing the USDA's SR22 nutritional database from MS Access to MySQL

hapviz. indel haplotype visualization on the command line from BAM files

wflign. the we-flyin WFA-guided ultralong tiling sequence aligner

dozyg. sequence to graph mapper

foxsamply. algorenderer / a script to convert FoxDot code to recorded samples

bitcoin-fs. encode arbitrary data in bitcoin transactions