stampy_indexer

stampy_indexer indexes reference genomes to support mapping of short DNA and RNA sequencing reads, enabling sensitive handling of substitutions and short insertions and deletions (indels).

Key Features:

• Hybrid Mapping Algorithm: Employs a hybrid mapping algorithm that integrates speed and sensitivity and is positioned relative to mappers such as BWA, Bowtie, ELAND, and Novoalign.
• Statistical Model: Incorporates a detailed statistical model to improve handling of sequence variation, particularly short insertions and deletions (indels).
• Improved Usable Sequence Yield and Accuracy: Enhances usable sequence yield and alignment accuracy when processing large sequencing datasets with variation.

Scientific Applications:

• Read origin inference: Supports inference of genomic origin for short reads from DNA and RNA sequencing experiments.
• High-throughput sequencing analysis: Applicable to large-scale DNA and RNA sequencing datasets requiring sensitive mapping.
• Divergent genome mapping: Suitable for mapping reads to highly divergent reference genomes where sequence variation is pronounced.

Methodology:

Implements a hybrid mapping algorithm combined with a detailed statistical model to balance speed and sensitivity and to handle substitutions and short indels.