TASR

TASR performs targeted assembly of reads from next-generation sequencing (NGS) datasets around user-provided target sequences to detect and characterize specific variants, fusion genes, and integration events without whole-genome assembly.

Key Features:

• Localized Assembly: Assembles only reads within the sequence space defined by user-provided target sequences, reducing analysis scope relative to whole-genome assembly.
• Exact Match Search: Searches for reads that exactly match all possible short words within the input target sequences to identify relevant reads.
• Stringent Assembly Process: Stringently assembles matching reads to generate consensus sequences of the target and its flanking regions.
• Variant Detection: Uses different target sequences representing alternate alleles to confirm or discover mutations, polymorphisms, fusion genes, and integration events at specific loci.
• Flexibility in Application: Identifies unknown sequences flanking a given target to enable discovery of novel adjacent sequences.

Scientific Applications:

• Mutation and Polymorphism Detection: Confirms or discovers specific mutations and polymorphisms within large NGS datasets.
• Disease Genetics and Personalized Medicine: Targets loci of clinical interest to support studies in disease genetics and personalized medicine.
• Evolutionary Biology: Enables targeted analysis of genetic variation relevant to evolutionary biology.
• Cancer Research: Detects fusion genes and integration events relevant to cancer research.
• Virology: Identifies viral integration events and fusion sequences relevant to virology.

Methodology:

TASR uses user-defined target sequences to search NGS datasets for reads that exactly match all possible short words within the targets and then stringently assembles those matching reads into consensus sequences encompassing the target and flanking regions.