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Updated: May 18, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application

Mark J Chaisson¹, Glenn Tesler

¹Department of Mathematics, University of California, San Diego, 9500 Gilman Dr, CA, La Jolla, USA.

BMC Bioinformatics

|September 20, 2012

Summary

This summary is machine-generated.

We developed BLASR, a fast and accurate method for mapping long DNA reads from Single Molecule Sequencing (SMS). This approach effectively handles the higher error rates in SMS data, improving genomic analysis.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

High-throughput DNA sequencing utilizes Single Molecule Sequencing (SMS) to generate reads up to tens of kilobases long.
Existing alignment methods struggle with the efficiency and accuracy required for SMS data due to its high error rate.

Purpose of the Study:

To introduce BLASR (Basic Local Alignment with Successive Refinement), an efficient and sensitive alignment tool for SMS reads.
To address the challenges posed by long reads and high error rates in SMS data.

Main Methods:

BLASR employs a novel algorithm for mapping long DNA sequences.
The method is designed to handle insertion and deletion errors prevalent in SMS reads.
A combinatorial model of sequencing error is presented to explain the method's effectiveness.

Main Results:

BLASR demonstrates high accuracy and speed in mapping SMS reads.
Benchmarking with simulated and real bacterial sequencing data validates the method's performance.
The combinatorial error model accurately predicts the observed mapping accuracy.

Conclusions:

It is feasible to achieve high-accuracy and high-speed mapping of Single Molecule Sequencing reads.
The developed combinatorial model provides insights into SMS read mapability.
BLASR offers a robust solution for analyzing long-read sequencing data.