zachcp / bioinformaticstoolkit

Build and deploy cross platform bioinformatic utilities with Rust.

The Bioinformatics Toolkit

RUST-backed utilities for bioinformatic data processing.

Get started

The fastest way to get started it to download the applications found in the Releasehttps://github.com/zachcp/bioinformaticstoolkit/releases section. This project aims to demonstrate how the Rust toolchain enables efficient cross-platform support for high-performance applications. By using Tauri you can write the entire frontend in any tool that compiles to HMLT+Javascript, in this case I used Quarto to take advantage of its simple composition (its mostly markdown +yaml) as well as it's built-in use of the observable runtime.

Screenshots

Below are screenshots of a native application demonstrating the home page, the guide page, an example RNA secondary strucutre visualization using rnapkin;statistics of a fasta file including a histrogram of sequence lengths using noodles for IO; and DNA translation using the protein_translation crate.

Develop

# assuming quarto and cargo are installed and on your path.
git clone https://github.com/zachcp/bioinformaticstoolkit.git
cd bioinformaticstoolkit

# install the tauri cli
cargo install tauri-cli

# add cargo bind dir to the path
export PATH=$PATH:~/.cargo/bin/

# to develop 
cargo-tauri dev

# to package. this build is ~8MB. 
cargo-tauri build

# to test
cd src-tauri && cargo test
# or verbose
cd src-tauri && cargo test -- --nocapture

Other Ideas/Tools for Rust Incorporation

FASTX:

• convert fasta to fastq
• basic stats of fasta/fastq
• histrogram of read lengths (possibly set max number)
• merge PE reads // split interleaved
• splitting into multiple files ( create directory ?)
• filter-fastx length // quality
• sample the fasta/x files
• plot: length x quality metrics ( optional hexagon plots )
• plot: coverage by location.

GFA:

• Utilites from GFATK including filtering
  • GFAStats

DNA Analysis:

• Digestability of DNA sequences:
  • Search for RE locations
  • Other Patterns to Avoid
  • Data: Standard RE enzymes
  • Plot: Genome View of RE sites.
  • Global view of Palettes and coding types
• Insilico PCR: https://github.com/dlesl/pcr
  • Clonifier: https://github.com/dlesl/clonifier
• Phenogram
• Pangenome TK: https://github.com/GeneDx/pgr-tk (cdep in the build)
• RE digest and assembly calculations

VCF:

• convert
• concat
• split

RNA Secondary Structure:

• RNApkin https://lib.rs/crates/rnapkin

rna-seq: - [ ] gencounts https://github.com/NKI-GCF/gensum - [ ] rust-lapper https://crates.io/crates/rust-lapper

Taxonomy:

• load and display a tree file
• load and display kraken
• load and display bracken

Peptides and Proteomics:

• unipept

Rust Software:

• Pangenomer
• rust-bio
• rust-bio-tools

Miscelleaneous:

• Genome Card: e.g viz with global genome statistics.
  • Genome name, overview, produces compounds
• Utilities for Codons
• VCF plotein
• ASGArt (cdep in the build)
• UDON
• GFAESTUS (c++ dep )
• BioSeq
• 10x Genomics Rust
• fq parser
• fastats
• fqmerge
• ggcat
• light motif
• liftover with crusmapr
• exon
• phylogeny # not much action
• chemical Reaction networks
• gb-io
• charming - a nive gui library
• met map
• barcode counter
• hpo
• nanopore read assessment: https://lib.rs/crates/nanoq#readme-read-report
• niffler
• OBO Validatio
• rustyms
• preotienogenic
• rdkit
• bigwig2bam
• Plasmapr: https://github.com/BradyAJohnston/plasmapR
• flate2use flate2::read::MultiGzDecoder;
• bio_streams
• Streaming iterators for bioinformatics data