Exacto

EXacto Accurate Characterization of Transcriptomes and genOmes

A long-read toolkit for mutant proteoform prediction. Exacto identifies somatic and germline DNA variants, RNA variants, integrates them, and translates full-length transcripts with variant annotation at the amino-acid level.

Documentation: https://pirl-unc.github.io/exacto/

01. Installation

Download the latest stable release here.

conda create -n exacto python=3.10
conda activate exacto
pip install pysam==0.23.0
conda install -c conda-forge rust==1.88.0
conda install -c anaconda pandas==2.2.3
conda install -c conda-forge polars==1.26.0
conda install -c conda-forge pyarrow==19.0.1
pip install exacto-<version>.tar.gz --verbose

A Docker image is also available on Docker Hub.

02. Dependencies

• Python (>=3.10)
• Rust (1.88.0 tested)
• numpy (>=1.22.3)
• pandas (>=2.0.3)
• polars (>=1.12.0)
• pyarrow (>=18.0.0)
• pysam (>=0.22.0)
• pytz (>=2024.1)

03. Usage

View all available subcommands

exacto --help

View a subcommand's parameters

exacto <subcommand> --help

Available subcommands

Subcommand	Description
annotate-vars	Annotate DNA or RNA variants with gene-level context.
build-genome-var-graph	Build a personalized genome variation graph.
build-transcriptome-var-graph	Build a personalized transcriptome variation graph.
call-germline-dna-vars	Call germline DNA variants from long-read alignments.
call-somatic-dna-vars	Call somatic DNA variants against matched control samples.
call-rna-vars	Call RNA variants from assembled transcript alignments.
call-peptide-vars	Call peptide-level variants from translated proteoforms.
integrate-vars	Integrate DNA and RNA variants into a unified callset.
remove-unspliced-rnas	Filter out unspliced (nascent) RNAs from a transcriptome assembly.
translate-seqs	Translate transcript sequences into peptide sequences.
translate-structs	Translate transcript structures into mutant proteoforms.

See the Commands documentation for full parameter documentation, and the Pipelines documentation for end-to-end mutant-proteoform-prediction and variation-graph-construction walkthroughs.

04. License

Licensed under the Apache License, Version 2.0.