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. 2010 Dec:Chapter 11:Unit 11.7.
doi: 10.1002/0471250953.bi1107s32.

Aligning short sequencing reads with Bowtie

Ben Langmead  1
Affiliations

Aligning short sequencing reads with Bowtie

Ben Langmead. Curr Protoc Bioinformatics. 2010 Dec.

Abstract

This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second-generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools.

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Figures

Figure 11.7.1
Figure 11.7.1
Sample Bowtie session. The last few lines are written to the “standard error” file handle and convey summary information about the run. The other lines are written to the “standard out” file handle and show valid, reportable alignments found by Bowtie. In this and subsequent figures, the backslash character is used to indicate that some long lines are wrapped.
Figure 11.7.2
Figure 11.7.2
Sample Bowtie session when SAM output mode is enabled. The last few lines are written to the “standard error” file handle and convey summary information about the run and are not part of the SAM format. The first few lines beginning with “@” are the SAM header. The remaining lines are alignments.
Figure 11.7.3
Figure 11.7.3
Listing of files output by bowtie-build after indexing the human sex chromosomes.
Figure 11.7.4
Figure 11.7.4
Output of bowtie-inspect when inspecting the index consisting of the two human sex chromosomes.
Figure 11.7.5
Figure 11.7.5
Output of the samtools consensus caller when calling SNPs from a simulated E. coli example dataset.
Figure 11.7.6
Figure 11.7.6
Bowtie output for previous example using −a and −v 2 options.
Figure 11.7.7
Figure 11.7.7
Bowtie output for previous example using −k 3 and −v 2 options.
Figure 11.7.8
Figure 11.7.8
Bowtie output for previous example using −k 6 and −v 2 options.
Figure 11.7.9
Figure 11.7.9
Bowtie output for previous example using just the −v 2 option.
Figure 11.7.10
Figure 11.7.10
Bowtie output for previous example using the --best, −a and −v 2 options.
Figure 11.7.11
Figure 11.7.11
Bowtie output for previous example using the −a and −m 5 and −v 2 options.
See this image and copyright information in PMC

References

    1. Burrows M, Wheeler DJ. A block sorting lossless data compression algorithm. Palo Alto, CA: Digital Equipment Corporation; 1994. Technical Report 124.
    1. Ferragina P, Manzini G. Opportunistic data structures with applications; Proceedings of the 41st Annual Symposium on Foundations of Computer Science; IEEE Computer Society; 2000.

    1. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. See above. Describes the indexing technique underlying the tool and compares to other alignment tools.

    1. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. - PMC - PubMed

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