Exacto

EXacto Accurate Characterization of Transcriptomes and genOmes

Exacto is a long-read toolkit for mutant proteoform prediction. Using long-read DNA and RNA sequencing data, Exacto:

• Identifies somatic and germline DNA variants.
• Performs variant-aware assembly of full-length transcripts.
• Identifies RNA variants.
• Links DNA and RNA variants.
• Translates transcripts into predicted proteoforms with amino acid-level annotations of DNA and RNA variants.
• Identifies mutant peptides against a reference proteome.

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==1.95.0
conda install -c conda-forge clangdev=21.1.8
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 (1.95.0 tested)
• libclang (>=9.0 and <22, build-time only — required by bindgen for the abPOA bindings)
• numpy (>=1.22.3)
• pandas (>=2.0.3)
• polars (>=1.12.0)
• pyarrow (>=18.0.0)
• pysam (>=0.22.0)
• pytz (>=2024.1)

Alignments must be made with minimap2 using --cs: exacto reads variants from the cs tag.

03. Usage

View all available subcommands

exacto --help

View a subcommand's parameters

exacto <subcommand> --help

Available subcommands

Subcommand	Description
cluster-rna-reads	Cluster long RNA reads by transcript of origin and call variants in each cluster.
correct-rna-reads	Error-correct RNA reads against the cluster each was assigned to.
determine-rna-consensus	Build one consensus sequence for each RNA read cluster.
stitch-reference-transcripts	Restore degraded transcript ends from the best-matching reference transcripts.
quantify-rna-abundances	Estimate per-cluster and per-reference-transcript abundances.
remove-unspliced-rnas	Remove unspliced RNAs from an RNA alignment.
call-germline-dna-vars	Call germline DNA variants from long-read alignments.
call-somatic-dna-vars	Call somatic DNA variants against one or more control samples.
call-rna-transcript-vars	Call RNA variants, transcript structures and nonsense-mediated decay predictions for assembled transcripts.
annotate-vars	Annotate DNA or RNA variants with gene-level context.
integrate-vars	Link RNA variants to DNA variants based on linear genomic / transcriptomic distances.
translate-transcripts	Translate assembled transcripts to proteoforms with DNA and RNA variants for each amino acid.
translate-seqs	Translate sequences in a FASTA / FASTQ file, or one sequence, to peptides.
call-peptide-vars	Call mutant peptides by comparing proteoforms with a reference proteome.
build-genome-var-graph	Build a personalized genome variation graph.
build-transcriptome-var-graph	Build a personalized transcriptome variation graph.

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.