Extract Transcript Sequences with gffread Element

This workflow element uses gffread to extract transcript sequences from provided genomic sequences and GFF/GTF annotation files.

Element type: gffread

Parameters

Parameter	Description	Default Value	Parameter in Workflow File	Type
Output sequences	Path to the output FASTA file with the extracted sequences.	(not set)	`url-out`	string

Name in GUI	Name in Workflow File	Slot	Slot in Workflow File	Type
`Input transcripts`	`in-data`	Genomic sequence URL	`genome`	string
		Transcripts URL	`transcripts`	string

Name in GUI	Name in Workflow File	Slot	Slot in Workflow File	Type
`Extracted sequences URL`	`extracted-data`	sequences	`sequences`	string

You can use this element in a workflow to extract coding sequences (CDS) or full transcript sequences using a reference genome and GFF/GTF file.

ugene workflow run \
  --element gffread \
  --genome genome.fa \
  --transcripts annotations.gtf \
  --url-out transcripts.fa

This will output transcripts.fa containing the sequences of all transcripts described in annotations.gtf, extracted from genome.fa.