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Liftoff Specifications

Process Details

  • Name: Liftoff
  • Process UUID: wlxiqqpp2zslu4caj3dmh70gfm9d1n
  • Process Group: Misc.

Overview

Liftoff is a tool for accurate mapping of annotations between genomes. It maps gene annotations from a reference genome to a target genome using sequence alignment and structural features. The process is particularly useful for transferring annotations between closely related genomes or different assemblies of the same genome.

This process is implemented in Bash, which invokes the Liftoff tool for genome annotation transfer.

Key Functionality

  • Annotation Transfer: Maps gene annotations from a reference genome to a target genome using sequence alignment
  • Feature Validation: Validates mapped features based on coverage and sequence identity thresholds
  • Structural Preservation: Maintains gene structure and relationships during the mapping process
  • Copy Detection: Optionally identifies additional gene copies in the target genome
  • Annotation Polish: Optionally refines annotations to restore proper coding sequences

Input/Output Specification

Inputs

Required Inputs

  • Target Genome FASTA

    • Description: Target genome sequence in FASTA format where annotations will be mapped
    • Format: FASTA

  • Reference Genome FASTA

    • Description: Reference genome sequence in FASTA format containing the original annotations
    • Format: FASTA

  • Reference Annotation GTF

    • Description: Gene annotations for the reference genome
    • Format: GTF

Optional Inputs

  • Chromosome List
    • Description: Text file containing chromosome names to restrict mapping
    • Format: TXT

Outputs

  • Mapped Annotations GTF
    • Description: Gene annotations mapped to the target genome
    • Format: GTF

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Minimap2 Parameters

    • Description: Space-delimited parameters for Minimap2
    • Default value: -a --end-bonus 5 --eqx -N 50 -p 0.5

  • A

    • Description: Designate a feature mapped only if it aligns with coverage greater than or equal to A
    • Default value: 0.5

  • S

    • Description: Designate a feature mapped only if its child features (usually exons/CDS) align with sequence identity greater than or equal to S
    • Default value: 0.5

  • Distance Scaling Factor

    • Description: Alignment nodes separated by more than a factor of distance scaling factor in the target genome will not be connected in the graph
    • Default value: 2.0

  • Flank

    • Description: Amount of flanking sequence to align as a fraction [0.0-1.0] of gene length. This can improve gene alignment where gene structure differs between target and reference
    • Default value: 0.0

  • Max Overlap

    • Description: Maximum fraction [0.0-1.0] of overlap allowed by 2 features
    • Default value: 0.1

  • Mismatch Penalty

    • Description: Mismatch penalty in exons when finding best mapping
    • Default value: 2

  • Gap Open Penalty

    • Description: Gap open penalty in exons when finding best mapping
    • Default value: 2

  • Gap Extend Penalty

    • Description: Gap extend penalty in exons when finding best mapping
    • Default value: 1

  • Polish Annotations

    • Description: Re-align the exons in attempt to restore proper coding sequences in cases where the lift-over resulted in start/stop codon loss or introduced an in-frame stop codon. This will increase run time, and may require 2-3x memory
    • Default value: false

  • Find Extra Copies

    • Description: Look for extra gene copies in the target genome
    • Default value: false

  • SC

    • Description: Minimum sequence identity in exons/CDS for which a gene is considered a copy; must be greater than -s
    • Default value: 1.0

References & Resources

  • Tool Documentation: Contact the team for details on the Liftoff implementation
  • Related Papers: Shumate, A. & Salzberg, S.L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021). https://doi.org/10.1093/bioinformatics/btaa1016