bwamem

Map sequence reads to reference genome using BWA

Since R2020b

Syntax

bwamem(indexBaseName,reads1,reads2,outputFileName)

bwamem(___,options)

bwamem(___,Name,Value)

Description

bwamem(indexBaseName,reads1,reads2,outputFileName) maps the sequencing reads from reads1 and reads2 against the reference sequence and writes the results to the output file outputFileName. The input indexBaseName represents the base name (prefix) of the reference index files [1][2].

bwamem 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.

bwamem(___,options) uses the additional options specified by options. Specify these options after all other input arguments.

bwamem(___,Name,Value) uses additional options specified by one or more name-value pair arguments. For example, 'BandWidth',90 sets the maximum allowable gap length to 90.

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

indexBaseName — Base name of reference index files

character vector | string

Base name (prefix) of the reference index files, specified as a character vector or string. For example, the base name of an index file 'Dmel_chr4.bwt' is 'Dmel_chr4'.

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

Example: 'Dmel_chr4'

Data Types: char | string

reads1 — Name of file with first mate reads or single-end reads

character vector | string

Name of the file with the first mate reads or single-end reads, specified as a character vector or string.

For paired-end data, the sequences in reads1 must correspond read-for-read to sequences in reads2.

Example: 'SRR6008575_10k_1.fq'

Data Types: char | string

reads2 — Name of file with second mate reads

character vector | string | []

Name of the file with the second mate reads, specified as a character vector or string.

Specify reads2 as empty ([], '', or "") if the data consists of single-end reads only.

Example: 'SRR6008575_10k_2.fq'

Data Types: char | string

outputFileName — Output file name

character vector | string

Output file name, specified as a character vector or string. This file contains the mapping results.

Example: 'SRR6008575_10k_chr4.sam'

Data Types: char | string

options — Additional options for mapping

BWAMEMOptions object | character vector | string

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

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: bwamem(indexbasename,reads1,reads2,outputfile,'BandWidth',90) sets 90 as the maximum allowable gap.

AlternativeHitsThreshold — Threshold for determining which hits receive XA tag in output SAM file

[5 200] (default) | nonnegative integer | two-element numeric vector

Threshold for determining which hits receive an XA tag in the output SAM file, specified as a nonnegative integer n or two-element numeric vector [n m], where n and m must be nonnegative integers.

If a read has less than n hits with a score greater than 80% of the best score for that read, all hits receive an XA tag in the output SAM file.

When you also specify m, the software returns up to m hits if the hit list contains a hit to an ALT contig.

Data Types: double

AppendReadCommentsToSAM — Flag to append FASTA or FASTQ comments to output SAM file

false (default) | true

Flag to append FASTA or FASTQ comments to the output SAM file, specified as true or false. The comments appear as text after a space in the file header.

Data Types: logical

BandWidth — Maximum allowable gap length

100 (default) | nonnegative integer

Maximum allowable gap length, specified as a nonnegative integer.

Data Types: double

BasesPerBatch — Number of bases per batch

[] (default) | positive integer

Number of bases per batch, specified as a positive integer.

If you do not specify BasesPerBatch, the software uses 1e7 * NumThreads by default. NumThreads is the number of parallel threads available when you run bwamem.

If you specify BasesPerBatch, the software uses that exact number and does not multiply the number by NumThreads. This rule applies regardless of whether you explicitly set NumThreads or not.

However, if you specify NumThreads but not BasesPerBatch, the software uses 1e7 * NumThreads.

The batch size is proportional to the number of parallel threads in use. Using different numbers of threads might produce different outputs. Specifying this option helps with the reproducibility of results.

Data Types: double

ClipPenalty — Penalty for clipped alignments

[5 5] (default) | nonnegative integer | two-element numeric vector

Penalty for clipped alignments, specified as a nonnegative integer or two-element numeric vector. Each read has the best score for an alignment that spans the length of the read. The software does not clip alignments that do not span the length of the read and do not score higher than the sum of ClipPenalty and the best score of the full-length read.

Specify a nonnegative integer to set the same penalty for both 5' and 3' clipping.

Specify a two-element numeric vector to set different penalties for 5' and 3' clipping.

Data Types: double

DropChainFraction — Threshold for dropping chains relative to longest overlapping chain

0.5 (default) | scalar between 0 and 1

Threshold for dropping chains relative to the longest overlapping chain, specified as a scalar between 0 and 1.

The software drops chains that are shorter than DropChainFraction * (longest overlapping chain length).

Data Types: double

DropChainLength — Minimum number of bases

0 (default) | nonnegative integer

Minimum number of bases in seeds forming a chain, specified as a nonnegative integer. The software drops chains shorter than DropChainLength.

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','-y'

Data Types: char | string

FastaHeaderToXR — Flag to include FASTA header in XR tag

false (default) | true

Flag to include the FASTA header in the XR tag, specified as true or false.

Data Types: logical

GapExtensionPenalty — Gap extension penalty

[1 1] (default) | nonnegative integer | two-element numeric vector

Gap extension penalty, specified as a nonnegative integer or two-element numeric vector [n m]. n is the penalty for extending a deletion. m is the penalty for extending an insertion.

If you specify a nonnegative integer, the software uses it as the penalty for extending a deletion or an insertion.

Data Types: double

GapOpenPenalty — Gap opening penalty

[6 6] (default) | nonnegative integer | two-element numeric vector

Gap opening penalty, specified as a nonnegative integer or two-element numeric vector [n m]. n is the penalty for opening a deletion. m is the penalty for opening an insertion.

If you specify a nonnegative integer, the software uses it as the penalty for opening a deletion or an insertion.

Data Types: double

HeaderInsert — Text to insert into header of output SAM file

[0x0 string] (default) | character vector | string

Text to insert into the header of the output SAM file, specified as a character vector or string.

Use one of the following:

• Character vector or string that starts with @ to insert the exact text to the SAM header

• Character vector or string that is a file name, where each line in the file must start with @

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 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 converts all available properties, using default values for unspecified properties. The only exception is when the default value of a property is NaN, Inf, [], '', or "". In this case, the software does not translate the corresponding property.

Data Types: logical

InsertSizeStatistics — Insert size distribution parameters

[1x0 double] (default) | four-element numeric array

Insert size distribution parameters, specified as a four-element numeric array [mean std max min].

• mean is the mean insert size.

• std is the standard deviation.

• max is the maximum insert size.

• min is the minimum insert size.

If you specify n elements array, where n is less than four, the elements specify the first n distribution parameters. By default, the software infers unspecified parameters from data.

Data Types: double

MarkShortSplitsSecond — Flag to mark shorter split hits as secondary

false (default) | true

Flag to mark the shorter split hits as secondary in the SAM flag, specified as true or false.

Data Types: logical

MarkSmallestCoordinatePrimary — Flag to mark segment with smallest coordinates as primary

false (default) | true

Flag to mark the segment with the smallest coordinates as primary when the alignment is split, specified as true or false.

Data Types: logical

MatchScore — Score for sequence match

1 (default) | nonnegative integer

Score for a sequence match, specified as a nonegative integer.

Data Types: double

MaxMemOccurrence — Maximum number of MEM occurrences

500 (default) | positive integer

Maximum number of MEM (maximal exact match) occurrences for each read before it is discarded, specified as a positive integer.

Data Types: double

MaxRoundsMateRescue — Maximum number of rounds of mate rescue

50 (default) | nonnegative integer

Maximum number of rounds of mate rescue for each read, specified as a nonnegative integer. The software uses the Smith-Waterman (SW) algorithm for the mate rescue.

Data Types: double

MinSeedLength — Minimum seed length

19 (default) | positive integer

Minimum seed length, specified as a positive integer. The software discards any matches shorter than the minimum seed length.

Data Types: double

MismatchPenalty — Penalty for alignment mismatch

4 (default) | nonnegative integer

Penalty for an alignment mismatch, specified as a nonnegative integer.

Data Types: double

NumThreads — Number of parallel threads

1 (default) | positive integer

Number of parallel threads to use, specified as a positive integer. Threads are run on separate processors or cores. Increasing the number of threads generally improves the runtime significantly, but increases the memory footprint.

Data Types: double

OutputAllAlignments — Flag to return all found alignments

false (default) | true

Flag to return all found alignments including unpaired and paired-end reads, specified as true or false. If the value is true, the software returns all found alignments and marks them as secondary alignments.

Data Types: logical

OutputScoreThreshold — Score threshold for returning alignments

30 (default) | positive integer

Score threshold for returning alignments, specified as a positive integer. Specify the minimum score that alignments must have to be in the output file.

Data Types: double

ReadGroupLine — Text to insert into read group header

[0x0 string] (default) | character vector | string

Text to insert into the read group (RG) header line in the output file, specified as a character vector or string.

Data Types: char | string

ReadType — Type of reads to align

[0x0 string] (default) | 'pacbio | 'ont2d | 'intractg'

Type of reads to align, specified as a character vector or string. Each read type has different default parameter values to use during alignment. You can overwrite any parameters. Valid options are:

• 'pacbio' — PacBio reads

• 'ont2d' — Oxford nanopore 2D reads

• 'intractg' — Intra-species contigs

The parameter values are as follows.

'pacbio'	MinSeedLength = 17 DropChainLength = 40 SeedSplitRatio = 10 MatchScore = 1 MismatchPenalty = 1 GapOpenPenalty = 1 GapExtensionPenalty = 1 ClipPenalty = 0 The equivalent native syntax is '-k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0'.
'ont2d'	MinSeedLength = 14 DropChainLength = 20 SeedSplitRatio = 10 MatchScore = 1 MismatchPenalty = 1 GapOpenPenalty = 1 GapExtensionPenalty = 1 ClipPenalty = 0 The equivalent native syntax is '-k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0'.
'intractg'	MismatchPenalty = 9 GapOpenPenalty = 16 ClipPenalty = 5 The equivalent native syntax is '-B9 -O16 -L5'.

Data Types: char | string

ReduceSupplementaryMAPQ — Flag to reduce mapping quality (MAPQ) score of supplementary alignments

true (default) | false

Flag to reduce the mapping quality (MAPQ) score of supplementary alignments, specified as true or false.

Data Types: logical

SeedSplitRatio — Threshold for reseeding

1.50 (default) | nonnegative integer

Threshold for reseeding, specified as a nonnegative integer. Specify the seed length at which reseeding happens relative to the minimum seed length MinSeedLength. Specifically, if a MEM (maximal exact match) is longer than MinSeedLength * SeedSplitRatio, reseeding occurs.

Data Types: double

SkipMateRescue — Flag to skip mate rescue

false (default) | true

Flag to skip mate rescue, specified as true or false. Mate rescue uses the Smith-Waterman (SW) algorithm to align unmapped reads with mates that are properly aligned.

Data Types: logical

SkipPairing — Flag to skip read pairing

false (default) | true

Flag to skip read pairing, specified as true or false. If true, for paired-end reads, the software uses the Smith-Waterman (SW) algorithm to rescue missing hits only and does not try to find hits that fit a proper pair.

Data Types: logical

SmartPairing — Flag to perform smart pairing

false (default) | true

Flag to perform smart pairing, specified as true or false. If the value is true, the software pairs adjacent reads that are in the same file and have the same name. Such FASTQ files are also known as interleaved files.

Data Types: logical

SoftClipSupplementary — Flag to soft clip supplemental alignments

false (default) | true

Flag to soft clip supplemental alignments, specified as true or false. If the value is true, the software soft clips both supplemental alignments and a primary alignment.

The default value is false, which means that the software soft clips the primary alignment and hard clips the supplemental alignments.

Data Types: logical

TreatAltAsPrimary — Flag to treat ALT contigs as part of primary assembly

false (default) | true

Flag to treat ALT contigs as part of the primary assembly, specified as true or false.

Data Types: logical

UnpairedReadPenalty — Penalty for mapping read pairs as unpaired

17 (default) | nonnegative integer

Penalty for mapping read pairs as unpaired, specified as a nonnegative integer.

The alignment score for a paired read pair is read1 score + read2 score - insert penalty. The alignment score for an unpaired read pair is read1 score + read2 score - UnpairedReadPenalty. The software compares these two scores to force read pairing. A larger UnpairedReadPenalty value leads to a more aggressive read pairing.

Data Types: double

Verbosity — Verbosity level of information printed

0 (default) | nonnegative integer

Verbosity level of information printed to the MATLAB command line while the software is running, specified as a nonnegative integer. Valid options are:

• 0 — For disabling all outputs to the command line.

• 1 — For printing error messages.

• 2 — For printing warning and error messages.

• 3 — For printing all messages.

• 4 — For debugging purposes only.

Data Types: double

ZDropOff — Cutoff for Smith-Waterman extension

100 (default) | nonnegative integer

Cutoff for the Smith-Waterman (SW) extension, specified as a nonnegative integer. The software uses the following expression:

$$\left|i-j\right|\ast MatchScore+ZDropOff$$, where i and j are the current positions of the query and reference, respectively. When the difference between the best score and current extension score is larger than this expression value, the software terminates the SW extension.

Data Types: double

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.

Version History

Introduced in R2020b