Commands

Reference for every Exacto command. For end-to-end walkthroughs that compose these into pipelines, see Pipelines. Every page is generated from the command’s own --help, so its flags and defaults are the ones the installed version accepts.

Variant-aware transcriptome assembly

Command	Description
cluster-rna-reads	Cluster long RNA reads by transcript of origin and call variants within 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.

Variant calling

Command	Description
call-germline-dna-vars	Call germline DNA variants in a long-read DNA BAM file.
call-somatic-dna-vars	Call somatic DNA variants in a case BAM file against one or more control BAM files.
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 the DNA variants that explain them.

Translation and peptides

Command	Description
translate-transcripts	Translate assembled transcripts to proteoforms, with variant provenance per amino acid.
translate-seqs	Translate sequences in a FASTA/FASTQ file, or one sequence, to peptide sequences.
call-peptide-vars	Call mutant peptides by comparing proteoforms with a reference proteome.

Variation graphs

Command	Description
build-genome-var-graph	Build a genome variation graph from DNA variant calls.
build-transcriptome-var-graph	Build a transcriptome variation graph from assembled transcript structures.