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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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libgapmis: extending short-read alignments.

Nikolaos Alachiotis, Simon Berger, Tomáš Flouri

BMC Bioinformatics

|February 26, 2014

Summary

This summary is machine-generated.

We introduce libgapmis, a new library for short-read alignment that efficiently handles gaps. It offers CPU, SSE, and GPU implementations, significantly accelerating computations for genomic analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Short-read alignment is crucial for mapping DNA sequences to reference genomes.
Existing alignment tools often struggle with accurately handling gaps in reads.
The seed-and-extend strategy is common, but extending alignments with gaps remains a challenge.

Purpose of the Study:

To develop an efficient library for extending pairwise short-read alignments, specifically addressing the challenge of gap handling.
To provide optimized implementations for accelerated alignment computations.
To offer flexibility in managing gaps within read alignments.

Main Methods:

Developed libgapmis, a library based on a modified dynamic programming algorithm for sequence alignment.
Implemented CPU, SSE, and GPU-accelerated versions of the alignment extension algorithm.
Enabled user-defined read fragmentation for flexible gap management.

Main Results:

libgapmis CPU version accelerates computations 20x compared to existing programs.
SSE and GPU implementations offer further speedups of 6x and 11x over the CPU version, respectively.
The library allows for variable, bounded numbers of gaps in alignments.

Conclusions:

libgapmis is a superior and more efficient tool for extending short-read alignments compared to existing methods.
The library's functions can be easily integrated into existing short-read alignment pipelines.
Open-source code is available for broader adoption and use in genomic research.