transmogR

transmogR provides tools to create a new reference genome or reference transcriptome using a set of variants.

Key Features:

• Variant Types Supported: Handles any combination of SNPs, insertions, and deletions.
• Reference Sequence Modification: Generates variant-modified reference transcriptomes from input reference sequences and variant sets.
• Workflow Integration: Enables incorporation of modified reference transcriptomes into transcriptomic pseudo-alignment workflows such as salmon.

Scientific Applications:

• Personalized Reference Transcriptome Construction: Creates sample-specific or population-specific reference transcriptomes for improved alignment accuracy.
• Transcriptomic Pseudo-alignment: Supports variant-aware quantification in transcriptomic analysis pipelines using tools such as salmon.

Methodology:

transmogR modifies reference sequences by applying a set of variants (SNPs, insertions, and deletions) to generate new reference genomes or transcriptomes.