Fulcrum Genomics

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 interfaces for reading, writing, and querying Genomic Regions (BED) in Python.
  • prymer: APIs and wrappers for performing PCR primer design and related tasks in Python.
• 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 and 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.