Nils Homer nh13

I improve human lives
by creating software
for biologists and clinicians
to accelerate breakthroughs in genomics science

🔬 I’m currently working on bioinformatics methods, tools, and pipelines
🧊 Open source is the tip of the iceberg — 💼 the rest is private for my clients at Fulcrum Genomics — 💍 keep it secret, keep it safe
📫 How to reach me:
🏢 See more code on or at

🧬 Open-source projects

Roles: A = author (originated it) · M = maintainer · C = contributor · F = former maintainer.

Project	Lang	Description	A	M
fgbio	Scala	Scala toolkit for UMI/consensus and NGS data manipulation	✅	✅
fqgrep	Rust	Grep for FASTQ files	✅	✅
DWGSIM	C	Whole-genome NGS read simulator with ground-truth variants for benchmarking	✅	✅
snakeparse	Python	Turn Snakemake workflows into command-line tools	✅	✅
fgumi	Rust	High-performance UMI tools for NGS	✅	✅
fgpyo	Python	Pythonic SAM/BAM, metrics, and sequence utilities	✅	✅
ref-solver	Rust	Identify which reference genome a BAM/CRAM used	✅	✅
fastquorum	Nextflow	Nextflow UMI consensus pipeline	✅	✅
ferro-hgvs	Rust	HGVS variant parser and normalizer	✅	✅
snakesee	Python	Terminal UI for monitoring Snakemake	✅	✅
fgsv	Scala	Structural-variation evidence tools	✅	✅
tricord	Rust	Report a process tree's CPU, memory, and I/O	✅	✅
singular-demux	Rust	Singular Genomics demultiplexer (sgdemux)	✅	✅
pybedlite	Python	Lightweight Python BED I/O	✅	✅
prymer	Python	Python primer design library	✅	✅
pybwa	Python	Python bindings for bwa	✅	✅
callerpp	C++	POA-based consensus caller	✅	✅
rebgzf	Rust	Fast gzip-to-BGZF transcoder	✅	✅
bwa-mem3	C++	Faster bwa-mem2 fork: correctness fixes, perf, single-binary methylation	✅	✅
mako	Rust	Fast SAM/BAM sorter	✅	✅
redskull	Rust	Conda recipe generator for Rust crates	✅	✅

Project	Lang	Description	M
htsjdk	Java	Java API for HTS formats	✅
fqtk	Rust	Fast FASTQ demultiplexing in Rust	✅
demultiplex	Nextflow	Nextflow demultiplexing and QC pipeline	✅
snakemake-aws-batch	Python	Snakemake AWS Batch executor plugin	✅

Project	Lang	Description	C
samtools	C	SAM/BAM/CRAM manipulation	✅
picard	Java	Java command-line tools for HTS data and formats	✅
minibwa	C	Minimal single-file bwa-mem implementation (by Heng Li)	✅

Project	Lang	Description	A	F
pbgzip	C	Parallel Block GZIP	✅	✅
TMAP	C	Ion Torrent read mapper	✅	✅
BFAST	C	BLAT-like Fast Accurate Search Tool	✅	✅
SRMA	C	Short-read micro-aligner	✅	✅