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
- 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
- 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.
