Eric T. Dawson

gfakluge. A C++ library and utilities for manipulating the Graphical Fragment Assembly format.

rkmh. Classify sequencing reads using MinHash.

mkmh. Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.

svaha2. Linear-time, low-memory construction of variation graphs

check-sex. Determine the biological sex of a human whole-genome BAM file

svaha. Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]

tidysig. A tidyverse-style package for plotting mutational signatures and context counts.

bam-matcher. Python

sv-exercise-1. A short exercise for learning to work with structural variants in VCF format

kseq_reader. A threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng Li

LaunChair. A small python utility which can execute a list of commands in parallel

gram. Parse, manipulate, and emit GRAM (graph read alignment/map format)

tinyGFA. A header-only GFA file indexer (think .fai for GFA files)

pliib. A hacky little C++ library that holds some useful functions.

biowulf-scripts. Scripts I use for analysis on NIH's Biowulf system.

ggsv. Simulation scripts and other items for comparing SV callers

seqmini. C++ code for creating minimizer indices on arbitrary FASTA / GFA

dawdl. WDL library for common bioinformatics tasks

kseqpp. Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

ntJoin. 🔗Genome assembly scaffolder using minimizer graphs

discohash. :dancers: Discohash - A super fast and simple hash. 5GB/s serial (depending on hardware).

sv-tutorial-2. A tutorial on calling structural variants with SVABA

rkmh2. Fast read filtering using MinHash

COSMIC2VCF. Convert various TSV files from the Catalogue of Somatic Mutations in Cancer to VCF (esp. structural variants)

presig. Convert MAF files to formats used as input to mutational signature programs including SigProfiler

tinyFA. A header-only C++ FASTA parser and indexer

bed2vcf. Convert a BED file (and a FASTA reference) to *mostly* valid VCF.

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

swarm. Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.

libVCFH. A small library for generating VCF headers