Possible Inclusion Ideas

[zachcp]

Rust BioTools

DNA FIle Processing

• FASTX:
  • convert fasta to fastq
  • basic stats of fasta/fastq
  • histogram 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
• VCF
• convert
• concat
• split
• Grumpy

DNA Analysis

• Digestibility 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
• Barcodes / Demultiplexing https://github.com/fulcrumgenomics/fqtk

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 Librarues

• Pangenomer
• rust-bio
• rust-bio-tools
• Slyph
• Alignoth

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
• BRICK Webapp
• Streaming iterators for bioinformatics data
• quickdna
• Conway-Bromage-Lyndon
• https://github.com/weng-lab/logojs-package
• fiber-seq

JS BioTools

• SGTK

• ribbon

• [jbrowse](https://jbrowse.org/jb2/docs/quickstart_web/

• ideogram

• genomegraphviewer

• https://github.com/stjude-rust-labs/ngs

• https://github.com/stjude-rust-labs/fq

• https://github.com/marschall-lab/panacus