Discover ekg/ogap Open Source project by Erik Garrison (@ekg)

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

208

alignment-and-variant-calling-tutorial

191

fraction.js

A fraction math library in javascript.

JavaScript

163

seqwish

alignment to variation graph inducer

utilities for indexing and sequence extraction from FASTA files

144

fastahack

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

bamaddrg

a string to graph aligner

glia

base-accurate DNA sequence alignments using edlib and mashmap2

thesis

my PhD thesis

TeX

edyeet

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

mmmulti

split and join for C++ strings

split

recompute GFA link overlaps

gimbricate

base-level dotplots from PAF alignments

pafplot

generate multiset combinations (n multichoose k)

multichoose

guix packages for bioinformatics software

guix-genomics

Scheme

HLA-zoo

genome variation graphs constructed from HLA GRCh38 ALTs

gafpack

convert variation graph alignments to coverage maps over nodes

haplotypes genotypes and alleles example decision synthesizer

hhga

efficient multiset permutations

multipermute

TypeScript

1000G-integration

variant integration methods for the 1000 Genomes Project

exploring viral genome assembly with variation graph tools

viral-assembly

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

shuntingyard

smith-waterman-gotoh alignment algorithm

smithwaterman

vector illustrations of BWT based searching on small strings

drawbwt

connect to a cisco anyconnect server with 2FA via web SSO on a headless server

openconnect-sso-docker

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

mutatrix

pca

PCA in rust

Prefix-renaming FASTA records really fast.

fastix

Yet another LLM command line interface

yllm

synchronous, serial, and parallel ssh, scp, and ping methods in python

ssh.py

encode arbitrary data in bitcoin transactions

bitcoin-fs

JavaScript

wflign

the we-flyin WFA-guided ultralong tiling sequence aligner

Day 2 of ACAD's 2018 Advanced Bioinformatics Workshop

ACAD18

dozyg

sequence to graph mapper

compressed, queryable variation graphs

succinct-graph

indel haplotype visualization on the command line from BAM files

hapviz

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

pafcheck

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

USDA-SR22-importer

split a FASTA sequence file into shorter sequences

splitfa

algorenderer / a script to convert FoxDot code to recorded samples

foxsamply

yeast-pangenome

loq

wflambda

WFλ - wavefront alignment with callback match function

binary kmers written numerically

bkmers

brute force online sequence similarity search

hamming-fasta

GAF (graph alignment format) command line utility

gaffy

zipfian int distributions using a fast approximation for pow

dirtyzipf

interleaves fastq files (also gzipped ones!)

interleave-fastq

snippets of music in foxdot

beats

rsvd

rSVD in rust

annotation of variants using genotype likelihoods

arfer

generate kmer frequency information from text streams

kmers

XBzip/XBWT implementation from "Compressing and indexing labeled trees, with applications," P Ferragina et al.

xbzipLib

jvcf

Joint Variant Call Format -- JSON notation for genetic variant annotation

bamprofile

profiles alignment mismatches and gaps

atomic bitset/bitvector with size determined at runtime

atomicbitvector

header-only large graph layout via stochastic gradient descent

sgd2

3q29 pangenome build from HPRC year 1 samples

3q29

pafcov

pairwise alignment file coverage metric

PAF alignment to network format converter

pafnet

exploring variation graph models for motifs based on partial order alignment

poa-motifs

paryfor

parallel_for based on atomic queues and C++11 threads

phred quality conversion to and from float and log space

phred.py

interval stabbing (pointwise range lookup) using the FastStabbing algorithm

intervalstab

exploring identity-based alignment chaining

edlign

use the cigar string in the PAF to correct target and query endpoint issues

pafciggy

a variation graph-oriented fork of WhatsHap

graphappy

A thread-safe LRU cache implementation in C++

lru_cache

aptertree

Apter Trees in rust

kmer counting comparisons in low memory

kmerj

entropy

shannon entropy

striped smith waterman implementation

ssw

simgenie

diplotype caller simulation on pangenie and freebayes

it's kind've like make, but not really. and it's for streams!

datscriptish

drosophila

drosophila genome assembly and analysis

tools for manipulating tab-separated-values files, mostly in C++

tsvtools

c++ header library for manipulating endianness

endian

uniqprimers

determines if the primers required to assay VCF records are unique (provided BAM alignments of the primers and a VCF file of the variants)

scripts for interpreting GFAs made by the shasta assembler

shastaGFA

an xml to .tsv converter for wikimedia XML data dumps

wikiq

demonstrates how to build leveldb with snappy support using the static libraries for each and git submodules

leveldb-snappy

compare call counts in two gprof profile outputs

gprof-compare

extensions for manipulating VCF files annotated with the Variant Annotation Tool (VAT)

vatfilter

query local LLM openai-API-compatible endpoints

qllm

split tsv files with headers

tsvsplit

nuller

null genotype caller which generates depth of coverage VCF

genmusic

pick an executable based on CPU capabilities

subarch-select

equal lists should serialize equally, but don't

bad-python-list

phage assembly and analysis scripts

phage

gatk-swe

Perl

factorial-ln

compute log(n!) of huge numbers

JavaScript

bamquality

read quality distributions for BAM and FASTQ files

command line tool to swap string patterns in text files

strswap

contig ordering using linkage disequilibrium

diatoms

embeddna

test of DNA embeddings using a transformer

analysis sketches for vertebrate genomes project assemblies

vgp

protobufstream

protocol buffers streams

stream a multiuser tidalcycles session

tidalcycles-stream

utility scripts and programs for manipulating fasta files

100

fasta-utilities