bwaindex

Create BWA indices from reference sequence

Syntax

bwaindex(referenceFile)

bwaindex(referenceFile,indexOptions)

bwaindex(referenceFile,Name,Value)

Description

bwaindex(referenceFile) creates BWA index files for the reference sequence in referenceFile [1][2]. By default, the function writes the index files to the same directory as referenceFile.

The index files are in the AMB, ANN, BWT, PAC, and SA file formats.

bwaindex requires the BWA Support Package for Bioinformatics Toolbox™. If the support package is not installed, then the function provides a download link. For details, see Bioinformatics Toolbox Software Support Packages.

Note

bwaindex is supported on the Mac and UNIX^® platforms only.

bwaindex(referenceFile,indexOptions) uses additional options specified by indexOptions.

bwaindex(referenceFile,Name,Value) uses additional options specified by one or more name-value pair arguments. For example, bwaindex(referenceFile,'Algorithm','is') specifies the linear-time algorithm.

Examples

Align Reads to Reference Sequence Using BWA

This example requires the BWA Support Package for Bioinformatics Toolbox™. If the support package is not installed, the software provides a download link. For details, see Bioinformatics Toolbox Software Support Packages.

Build a set of index files for the Drosophila genome. This example uses the reference sequence Dmel_chr4.fa, provided with the toolbox. The 'Prefix' argument lets you define the prefix of the output index files. You can also include the file path information. For this example, define the prefix as Dmel_chr4 and save the index files in the current directory.

bwaindex('Dmel_chr4.fa','Prefix','./Dmel_chr4');

As an alternative to specifying name-value pair arguments, you can use the BWAIndexOptions object to specify the indexing options.

indexOpt = BWAIndexOptions;
indexOpt.Prefix = './Dmel_chr4';
indexOpt.Algorithm = 'bwtsw';
bwaindex('Dmel_chr4.fa',indexOpt);

Once the index files are ready, map the read sequences to the reference using bwamem. Two pair-end read input files are already provided with the toolbox. Using name-value pair arguments, you can specify different alignment options, such as the number of parallel threads to use.

bwamem('Dmel_chr4','SRR6008575_10k_1.fq','SRR6008575_10k_2.fq','SRR6008575_10k_chr4.sam','NumThreads',4);

Alternatively, you can use BWAMEMoptions to specify the alignment options.

alignOpt = BWAMEMOptions;
alignOpt.NumThreads = 4;
bwamem('Dmel_chr4','SRR6008575_10k_1.fq','SRR6008575_10k_2.fq','SRR6008575_10k_chr4.sam',alignOpt)

Input Arguments

referenceFile — Reference file name

character vector | string

Reference file name, specified as a character vector or string. The file must be a FASTA-formatted file with the reference sequence information for indexing.

Data Types: char | string

indexOptions — Additional options for indexing

BWAIndexOptions object | character vector | string

Additional options for indexing, specified as a BWAIndexOptions object, character vector, or string. The character vector or string must be in the bwa index native syntax (prefixed by a dash). If you specify a BWAIndexOptions object, the function uses only those properties that are set or modified.

Data Types: char | string

Name-Value Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside quotes. You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

Example: bwaindex(referenceFile,'Algorithm','bwtsw') specifies to use the BWT-SW algorithm.

'Algorithm' — Algorithm to construct BWT index

'is' | 'bwtsw'

Algorithm to construct the BWT (Burrows-Wheeler transform) index, specified as a character vector or string. Options are:

• 'is' — Linear-time algorithm. The memory requirement for using this option is 5.37 times the size of the database. You cannot use this option if your database is larger than 2 GB.

• 'bwtsw' — BWT-SW algorithm.

The default algorithm is chosen automatically based on the size of the reference genome.

Data Types: char | string

'BlockSize' — Number of bases processed per batch

1e7 (default) | positive scalar

Number of bases processed per batch in the bwtsw algorithm, specified as a positive scalar.

Data Types: double

'ExtraCommand' — Additional commands

"" (default) | character vector | string

Additional commands, specified as a character vector or string.

The commands must be in the native syntax (prefixed by one or two dashes). Use this option to apply undocumented flags and flags without corresponding MATLAB^® properties.

Example: 'ExtraCommand','-6'

Data Types: char | string

'IncludeAll' — Flag to apply all available options

false (default) | true

Flag to include all available options with the corresponding default values when converting to the original options syntax, specified as true or false.

The original (native) syntax is prefixed by one or two dashes. By default, the function converts only the specified options. If the value is true, the software converts all available options, with default values for unspecified options, to the original syntax.

Note

If you set IncludeAll to true, the software translates all available properties, with default values for unspecified properties. The only exception is that when the default value of a property is NaN, Inf, [], '', or "", then the software does not translate the corresponding property.

Example: 'IncludeAll',true

Data Types: logical

'Prefix' — Prefix for output index files

character vector | string

Prefix for the output index files, specified as a character vector or string. You can specify only the prefix or a file path and prefix. The default value is the same as the input FASTA file name.

Example: 'Prefix','D:/ngs/GRCh38_p12'

Data Types: char | string

References

[1] Li, Heng, and Richard Durbin. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25, no. 14 (July 15, 2009): 1754–60. https://doi.org/10.1093/bioinformatics/btp324.

[2] Li, Heng, and Richard Durbin. “Fast and Accurate Long-Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 26, no. 5 (March 1, 2010): 589–95. https://doi.org/10.1093/bioinformatics/btp698.