Aligning Short Sequencing Reads with Bowtie
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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. Curr. Protoc. Bioinform. 32:11.7.1?11.7.14. © 2010 by John Wiley & Sons, Inc.
Keywords: short reads; read alignment; alignment; read mapping; mapping; genome indexing; comparative genomics; software package
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Aligning a Set of Short Reads to a Reference Genome
- Alternate Protocol 1: Building an Index for a Set of Reference Sequences
- Alternate Protocol 2: Alignment and Variation Detection Using Bowtie and SAMtools
- Alternate Protocol 3: Running Bowtie with Various Command‐Line Options
- Support Protocol 1: Obtaining and Installing the Bowtie Package
- Support Protocol 2: Building Bowtie from Source
- Support Protocol 3: Downloading and Installing a Prebuilt Bowtie Index
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 11.7.1 Sample Bowtie session. The last few lines are written to the standard error file handle and they 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. View Image -
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. View Image -
Figure 11.7.3 Listing of files output by bowtie‐build after indexing the human sex chromosomes. View Image -
Figure 11.7.4 Output of bowtie‐inspect when inspecting the index consisting of the two human sex chromosomes. View Image -
Figure 11.7.5 Output of the SAMtools consensus caller when calling SNPs from a simulated E. coli example dataset. View Image -
Figure 11.7.6 Bowtie output for the previous example using ‐a and ‐v 2 options. View Image -
Figure 11.7.7 Bowtie output for the previous example using ‐k 3 and ‐v 2 options. View Image -
Figure 11.7.8 Bowtie output for the previous example using ‐k 6 and ‐v 2 options. View Image -
Figure 11.7.9 Bowtie output for the previous example using just the ‐v 2 option. View Image -
Figure 11.7.10 Bowtie output for the previous example using the ‐‐best, ‐a, and ‐v 2 options. View Image -
Figure 11.7.11 Bowtie output for the previous example using the ‐a and ‐m 5 and ‐v 2 options. View Image
Videos
Literature Cited
| Burrows, M. and Wheeler, D.J. 1994. A block sorting lossless data compression algorithm. Technical Report 124. Digital Equipment Corporation, Palo Alto, Calif. | |
| Cock, P.J., Fields, C.J., Goto, N., Heuer, M.L., and Rice, P.M. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 38:1767‐1771. | |
| Ferragina, P. and Manzini, G. 2000. Opportunistic data structures with applications. In Proceedings of the 41st Annual Symposium on Foundations of Computer Science. IEEE Computer Society. | |
| Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. 2009. Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. | |
| Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078‐2079. | |
| Key Reference | |
| Langmead et al., 2009. See above. | |
| Describes the indexing technique underlying the tool and compares to other alignment tools. | |
| Internet Resource | |
| http://bowtie‐bio.sf.net | |
| The project's home page where the latest version of the package can be downloaded and where announcements are made. |
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