Roadmap: Planned Features & Milestones

[LCrossman]

Core Infrastructure
using Async where possible, parsing bioinformatic file types

• Genbank parser
• Embl parser
• Conversions of formats into gbk/embl/fasta/ffn/faa and save as gff/gbk or embl
• CI/CD with github actions and write tests - ongoing
• Documentation with examples - ongoing

Format expansion
Integration of common types and parsers such as:

• VCF
• BLAST output in various modes, -5 (XML) and -6 (one line per hit), compat with Diamond, MMSeqs2
• GTF
• link ups with formats from rust-bio, noodles-vcf
• look into metabolomics options (like KEGG) some are not open-source
• fastq gzipped version parsing
• SAM format parser
• RPKM output parser
• Support for other compressed files such as BAM and CRAM
• Writer support for those types

Advanced features
Protein parameters such as:

• Hydrophobicity
• Molecular weight
• Counted amino acids & as percentage
• Aromaticity
• Parsing phylogenetic trees
• Parsing multiple sequence alignments
• Methylation data parsing
• Consider pyo3 integration

Testing - bioinformatics

• Testing & updating parsers with various edge case files such as gbk with the CONTIG(JOIN) structure

Data Viz

• Example heatmap with WASM and Js example
• Simple graph types bar, line, scatter