Hash table

Gene

Algorithm

Biology

Alignment-free sequence analysis

Hash function

Reference genome

Operating system

Data mining

Computer science

DNA sequencing

Hybrid genome assembly

Single-nucleotide polymorphism

Software

Genetics

Sequence (biology)

Genotype

Multiple sequence alignment

Sequence alignment

Programming language

Peptide sequence

Indel

Smith–Waterman algorithm

Bioinformatics

Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time.We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both.http://bio-bwa.sourceforge.net

Fast and accurate short read alignment with Burrows–Wheeler transform