Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

Abstract excerpt

MOTIVATION: Mapping billions of reads from next generation sequencing experiments to reference genomes is a crucial task, which can require hundreds of hours of running time on a single CPU even for the fastest known implementations. Traditional approaches have difficulties dealing with matches of large edit distance, particularly in the presence of frequent or large insertions and deletions (indels). This is a...

Topics

Share this publication in a Topic to start or enrich a Post.

• Share to Chromosome Mapping
• Share to Genetic Variation
• Share to Genome, Human