Fulcrum Genomics Speaks Biology.

We are bioinformaticians, computational biologists, and software engineers with experience in basic research, technology development, diagnostics, therapeutics and beyond. Talk to us about your problem –- we’ll understand.

Below are Toolkits, Libraries, and Template Repositories that we've developed and use on a regular basis. We hope that you will find them useful too!

• We prefer to publish under the MIT License; Forked repositories normally retain their original license and thus may be published under a different license.
• We have a Code of Conduct

Here are some toolkits we've developed:

• fgbio: Tools for working with genomic and high throughput sequencing data in Scala.
• fgsv: Tools to gather evidence for structural variation via breakpoint detection.
• fqtk: Fast FASTQ sample demultiplexing in Rust.
• fqgrep: Grep for FASTQ files.
• stitch: Stitch is a toolkit for analysis of chimeric reads in sequencing data.
• guide-counter: A better, faster way to count guides in CRISPR screens.
• bwa: A fork of bwa to run interactively and work with bwa on the command line.

Here are some libraries that we use regularly in our work:

• Python
  • fgpyo: Quality of life improvements for Bioinformatics in Python.
  • pybedlite: Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED).
• Rust
  • fgoxide: Quality of life improvements for Bioinformatics in Rust.
  • read-structure: Read structures in rust.
  • pooled-writer: A pooled writer and compressor library in Rust.
  • bgzf: High level readers and writers for the BGZF format in Rust.
• Scala
  • fgprimer: APIs and wrappers for performing PCR primer design related tasks in Scala.
  • sopt: An argument parsing library for Scala.
  • commons: A collection of useful libraries for Scala.
• GitHub Actions
  • setup-latch: A GitHub action for building and register Latch Bio workflows.

Here are some template repositories we use when we start something new:

• python-snakemake-template: A template repository for Snakemake pipepline(s) and a python command-line toolkit.