About Fulcrum.

Our team has authored more than 500 peer-reviewed papers, cited over 200,000 times.

We wrote the methods papers your field depends on.

Built by scientists, for scientists.

Founded by computational biologists from the Broad Institute, Fulcrum brings production genomics expertise to biotech and pharma companies.

We’ve spent years solving hard problems at scale — from foundational methods for UMI-based analysis to custom pipelines for genome editing — and we bring that experience to your work.

Research & standards

The Broad Institute

Academic genomics groups

Industry & clinical

Ultra-accurate sequencing startups

Clinical diagnostics labs

Sequencing cores

500+Peer-reviewed publications

200,000+Citations across the team

11+Years founder-owned & independent

Foundational work.

Before founding Fulcrum, our team helped build the standards and tools the field runs on.

Bioinformatics2009

First page of: The Sequence Alignment/Map format and SAMtools

view paper

Bioinformatics · 2009The Sequence Alignment/Map format and SAMtools

Defined the SAM/BAM format, among the most-cited papers in bioinformatics.

Li H, Handsaker B, Wysoker A, Tim Fennell, Ruan J, Nils Homer, et al.

Bioinformatics2011

First page of: The variant call format and VCFtools

view paper

Bioinformatics · 2011The variant call format and VCFtools

Defined the VCF standard used across genomics.

Danecek P, Auton A, … Durbin R, and the 1000 Genomes Project Analysis Group — incl. Nils Homer, Tim Fennell

PLoS Genetics2008

First page of: Resolving individuals contributing trace amounts of DNA to highly complex mixtures

view paper

PLoS Genetics · 2008Resolving individuals contributing trace amounts of DNA to highly complex mixtures

The genomic-privacy result that changed NIH policy on aggregate GWAS data.

Nils Homer, Szelinger S, Redman M, … Craig DW

Work with the people who wrote it

Recent publications.

Our team contributes to peer-reviewed research across genomics, diagnostics, therapeutics, and technology development.

arXiv2026

First page of: Fast genomic read alignment with minibwa

view paperarXiv · 2026Fast genomic read alignment with minibwa

Heng Li, Nils Homer

bioRxiv2026

First page of: Expanded unbiased population-genomic summary statistics in pixy

view paperbioRxiv · 2026Expanded unbiased population-genomic summary statistics in pixy

K. Samuk, Matt Stone, Erin McAuley, et al.

bioRxiv2026

First page of: Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

view paperbioRxiv · 2026Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

H. Colegrove, … Zach Norgaard, Clint Valentine, et al.

NAR Molecular Medicine2026

First page of: Evaluation of ensilication technology for ambient DNA preservation

view paperNAR Molecular Medicine · 2026Evaluation of ensilication technology for ambient DNA preservation

M. Blas, … Nils Homer, et al.

bioRxiv2026

First page of: Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

view paperbioRxiv · 2026Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

T. Xu, … Yossi Farjoun, et al.

Nature Genetics2026

First page of: Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling

view paperNature Genetics · 2026Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling

A. Krishna, Alison Meynert, et al.

Bioinformatics Advances2025

First page of: MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology

view paperBioinformatics Advances · 2025MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology

A. Dodge, … Clint Valentine, et al.

bioRxiv2024

First page of: Large serine integrase off-target discovery and validation for therapeutic genome editing

view paperbioRxiv · 2024Large serine integrase off-target discovery and validation for therapeutic genome editing

D. Hazelbaker, … Tim Fennell, Nils Homer, et al.

Nature2024

First page of: A genomic mutational constraint map using variation in 76,156 human genomes (gnomAD v4)

view paperNature · 2024A genomic mutational constraint map using variation in 76,156 human genomes (gnomAD v4)

gnomAD Consortium — incl. Yossi Farjoun, Jeff Gentry, Charlotte Tolonen

Nature Communications2023

First page of: vcfdist: accurately benchmarking phased small variant calls in human genomes

view paperNature Communications · 2023vcfdist: accurately benchmarking phased small variant calls in human genomes

Tim Dunn, et al.

FSI: Genetics2022

First page of: Fast and accurate kinship estimation using sparse SNPs in relatively large database searches

view paperFSI: Genetics · 2022Fast and accurate kinship estimation using sparse SNPs in relatively large database searches

J. Snedecor, Tim Fennell, S. Stadick, Nils Homer, et al.

The CRISPR Journal2021

First page of: CALITAS: A CRISPR-Cas-aware Aligner for In silico off-Target Search

view paperThe CRISPR Journal · 2021CALITAS: A CRISPR-Cas-aware Aligner for In silico off-Target Search

Tim Fennell, D. Zhang, M. Isik, et al.

Open Source

Release early. Release often. And listen to your customers.

Every stage of a read's journey runs through tools our team builds or has merged code into. If you've run a sequencing pipeline, you've run our code.

tools we build projects we help maintain authored by our people merged contributions

tap a station to see the receipts · or expand all

The people who maintain the field's infrastructure are the people who'll work on your pipeline.

Tools we buildfgbio ↗Tools for working with genomic and high-throughput sequencing data.fqgrep ↗Grep for FASTQ files.fqtk ↗Fast FASTQ sample demultiplexing in Rust.riker ↗A spiritual successor to Picard for sequencing QC.fgumi ↗High-performance UMI tools for NGS data analysis.guide-counter ↗A better, faster way to count guides in CRISPR screens.ferro-hgvs ↗High-performance HGVS variant nomenclature parser and normalizer.bwa-mem3 ↗Accelerated short-read alignment derived from bwa-mem2 — a drop-in replacement.dupblaster ↗Blazingly fast, streaming duplicate detection for NGS data.fgsv ↗Evidence-gathering for structural variation via breakpoint detection.mako ↗Fast SAM/BAM sorter.methylsieve ↗Fast, robust filtering of unconverted reads in methylation sequencing.And merged into, across the fieldBioconda htsjdk modules picard pysam cuda-oxide tools samtools MultiQC Kraken 2 nextflow snakemake fastp WDL / OpenWDL conda-forge Data Carpentry minibwa VerifyBamID GLIMPSE CIViCpy libdeflate Exomiser cromwell hts-specs cyvcf2 fastquorum sassy latch kuva permutect pf-curie TMB pixy Broad TAG noodles bioconda-utils hgvs-rs sandbox.bio fastqc-rs geneimpacts Mutalyzer rust-htslib snakemake AWS-Batch magicjar defopt bio-seq seq_io superintervals libsais

Meet the team.

Tim Fennell, BSc

Founding Partner

Boulder, CO

NGS tools and pipelines for molecular biology debugging

Publications

Nils Homer, PhD

Founding Partner

Phoenix, AZ

Algorithms for alignment, error-corrected sequencing, and novel technologies

Publications

Clint Valentine, MS

Vice President, Operations

Hawaii

Ultra-accurate sequencing, biotech startups, and cancer research

Publications

Juliann Chmielecki, PhD

Vice President, Translational Research

Boston, MA

Translational cancer research, genomics, precision medicine, and NGS diagnostics

Publications

Tim Dunn, PhD

Staff Bioinformatics Engineer

Michigan

Alignment algorithms and variant call benchmarking

Publications

Jason Fan, PhD

Staff Bioinformatics Engineer

Virginia

NGS algorithms and pipelines, single-cell and RNAseq

Publications

Yossi Farjoun, PhD

Principal Bioinformatics Scientist

Montreal, Quebec, Canada

Algorithms, machine learning, and statistics for NGS signal and QC

Publications

Jeff Gentry, MS

Distinguished Bioinformatics Engineer

Somerville, MA

Software & data engineering, data platform development, and real-world data

Publications

Erin McAuley, PhD

Staff Bioinformatics Scientist

Virginia

Clinical genetics and NGS variant analysis workflows

Publications

Alison Meynert, PhD

Principal Bioinformatics Scientist

British Columbia, Canada

Variant annotation, clinical classification, data integration

Publications

Zach Norgaard, PhD

Associate Director Bioinformatics

Seattle, WA

New product development and efficiency in a regulated environment

Publications

Jess Smith, PhD

Principal Bioinformatics Scientist

Somerville, MA

Sequencing technology and assay development

Publications

Matt Stone, MS

Associate Director of Engineering

New Jersey

Therapeutic discovery pipelines and sequencing data analysis

Publications

Charlotte Tolonen, MSc

Chief of Staff

Paris, France

Data operations and large-scale collaborations

Publications

About Fulcrum.

Built by scientists, for scientists.

Research & standards

Industry & clinical

Foundational work.

Recent publications.

Release early. Release often. And listen to your customers.

Teaching

Beyond bio

Meet the team.

Get in touch to see how we can help you.

About Fulcrum.

Built by scientists, for scientists.

Research & standards

Industry & clinical

Foundational work.

Recent publications.

Release early. Release often. And listen to your customers. [1]

Teaching

Beyond bio

Meet the team.

Get in touch to see how we can help you.

Release early. Release often. And listen to your customers.