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. 2009;10(3):R25.
doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead  1 , Cole Trapnell, Mihai Pop, Steven L Salzberg
Affiliations

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al. Genome Biol. 2009.

Abstract

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).

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Figures

Figure 1
Figure 1
Burrows-Wheeler transform. (a) The Burrows-Wheeler matrix and transformation for 'acaacg'. (b) Steps taken by EXACTMATCH to identify the range of rows, and thus the set of reference suffixes, prefixed by 'aac'. (c) UNPERMUTE repeatedly applies the last first (LF) mapping to recover the original text (in red on the top line) from the Burrows-Wheeler transform (in black in the rightmost column).
Figure 2
Figure 2
Exact matching versus inexact alignment. Illustration of how EXACTMATCH (top) and Bowtie's aligner (bottom) proceed when there is no exact match for query 'ggta' but there is a one-mismatch alignment when 'a' is replaced by 'g'. Boxed pairs of numbers denote ranges of matrix rows beginning with the suffix observed up to that point. A red X marks where the algorithm encounters an empty range and either aborts (as in EXACTMATCH) or backtracks (as in the inexact algorithm). A green check marks where the algorithm finds a nonempty range delimiting one or more occurrences of a reportable alignment for the query.
Figure 3
Figure 3
The three phases of the Bowtie algorithm for the Maq-like policy. A three-phase approach finds alignments for two-mismatch cases 1 to 4 while minimizing backtracking. Phase 1 uses the mirror index and invokes the aligner to find alignments for cases 1 and 2. Phases 2 and 3 cooperate to find alignments for case 3: Phase 2 finds partial alignments with mismatches only in the hi-half, and phase 3 attempts to extend those partial alignments into full alignments. Finally, phase 3 invokes the aligner to find alignments for case 4.
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Comment in

  • The need for speed.
    Flicek P. Flicek P. Genome Biol. 2009;10(3):212. doi: 10.1186/gb-2009-10-3-212. Epub 2009 Mar 27. Genome Biol. 2009. PMID: 19344490 Free PMC article.

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