Introduction

The Rbwa package provides an R wrapper around the two popular BWA aligners BWA-backtrack (Li and Durbin 2009) and BWA-MEM (Li 2013).

As mentioned in the BWA manual (see http://bio-bwa.sourceforge.net/bwa.shtml), BWA-backtrack is designed for short Illumina reads (up to 100bp), while BWA-MEM is more suitable for longer sequences (70bp to 1Mbp) and supports split alignment.

Installation

Rbwa can be installed from Bioconductor using the following commands in a fresh R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rbwa")

Overview

The two main alignment functions are:

BWA-backtrack: bwa_aln
BWA-MEM: bwa_mem

The package also includes the following convenience functions:

Genome indexing: bwa_build_index
Conversion of bwa_aln output into SAM output: bwa_sam
Generation of secondary alignments: xa2multi

Build a reference index with `bwa_build_index`

Both bwa_aln and bwa_mem require first to create a genome index from a FASTA file. This is done only once for a given genome. This can be done using the function bwa_build_index.

First, we load Rbwa:

library(Rbwa)

In the following example code, we build a BWA index for a small portion of human chr12 that we stored in a FASTA file located within the Rbwa package. We store the index files in a temporary directory.

dir <- tempdir()
fasta <- system.file(package="Rbwa",
                     "fasta/chr12.fa")
index_prefix <- file.path(dir, "chr12")
bwa_build_index(fasta,
                index_prefix=index_prefix)
list.files(dir)

## [1] "chr12.amb" "chr12.ann" "chr12.bwt" "chr12.pac" "chr12.sa"

Aligment with `bwa_aln`

We now align read sequences stored in the toy example FASTQ file fastq/sequences.fastq, provided in the Rbwa package, to our indexed genome:

fastq <- system.file(package="Rbwa",
                     "fastq/sequences.fastq")
bwa_aln(index_prefix=index_prefix,
        fastq_files=fastq,
        sai_files=file.path(dir, "output.sai"))

Any valid BWA arguments can be passed to the bwa_aln function. To see the complete list of valid arguments, please visit the BWA reference manual: http://bio-bwa.sourceforge.net/bwa.shtml.

For instance, we can specify the maximal edit distance between the query sequence and the reference genome to be 3 using n, as well as the maximal edit distance in the seed sequence k to be 3, where we specify that the length of the seed sequence is 13 using the argument l:

bwa_aln(index_prefix=index_prefix,
        fastq_files=fastq,
        sai_files=file.path(dir, "output.sai"),
        n=3, k=3, l=13)

Creating a SAM file

The output of bwa_aln is an intermediate sai file that should be converted into a sam file using the bwa_sam function as follows:

bwa_sam(index_prefix=index_prefix,
        fastq_files=fastq,
        sai_files=file.path(dir, "output.sai"),
        sam_file=file.path(dir, "output.sam"))

Let’s read the first few lines of the SAM file:

strtrim(readLines(file.path(dir, "output.sam")), 65)

## [1] "@SQ\tSN:chr12\tLN:171330"                                                             
## [2] "@PG\tID:bwa\tPN:bwa\tVN:0.7.17-r1198-dirty\tCL:/tmp/RtmpRt1Iia/Rinst95016"            
## [3] "ACATCAGAAAGAGCGGCAG\t0\tchr12\t170881\t37\t19M\t*\t0\t0\tACATCAGAAAGAGCGGCAG\t~~~~~~~"
## [4] "CAACCCAGCCCCCCTCCAA\t0\tchr12\t170801\t37\t19M\t*\t0\t0\tCAACCCAGCCCCCCTCCAA\t~~~~~~~"
## [5] "CCTGTGATCCACGGAGGCT\t0\tchr12\t170765\t37\t19M\t*\t0\t0\tCCTGTGATCCACGGAGGCT\t~~~~~~~"
## [6] "GCACTGCGGTGAGTGCTGT\t0\tchr12\t170665\t37\t19M\t*\t0\t0\tGCACTGCGGTGAGTGCTGT\t~~~~~~~"
## [7] "GCCTTTTACAGTTCGTACT\t0\tchr12\t170820\t37\t19M\t*\t0\t0\tGCCTTTTACAGTTCGTACT\t~~~~~~~"
## [8] "GTCATGCCCCCTCAGCCAG\t0\tchr12\t170703\t37\t19M\t*\t0\t0\tGTCATGCCCCCTCAGCCAG\t~~~~~~~"
## [9] "TCGGCTCTCACCGTGTCCG\t0\tchr12\t170646\t37\t19M\t*\t0\t0\tTCGGCTCTCACCGTGTCCG\t~~~~~~~"

Creating a SAM file with secondary alignments

By default, each row of the SAM output corresponds to the best alignment hit for a given input query sequence. Other alignments (secondary alignments, or other loci in case of multiple alignments) are stored in the XA tag.

The function xa2multi conveniently extracts the alignments from the XA tags and represent them as additional rows in the SAM format. This can be executed as follows:

xa2multi(file.path(dir, "output.sam"),
         file.path(dir, "output.multi.sam"))
strtrim(readLines(file.path(dir, "output.multi.sam")), 65)

## [1] "@SQ\tSN:chr12\tLN:171330"                                                             
## [2] "@PG\tID:bwa\tPN:bwa\tVN:0.7.17-r1198-dirty\tCL:/tmp/RtmpRt1Iia/Rinst95016"            
## [3] "ACATCAGAAAGAGCGGCAG\t0\tchr12\t170881\t37\t19M\t*\t0\t0\tACATCAGAAAGAGCGGCAG\t~~~~~~~"
## [4] "CAACCCAGCCCCCCTCCAA\t0\tchr12\t170801\t37\t19M\t*\t0\t0\tCAACCCAGCCCCCCTCCAA\t~~~~~~~"
## [5] "CCTGTGATCCACGGAGGCT\t0\tchr12\t170765\t37\t19M\t*\t0\t0\tCCTGTGATCCACGGAGGCT\t~~~~~~~"
## [6] "GCACTGCGGTGAGTGCTGT\t0\tchr12\t170665\t37\t19M\t*\t0\t0\tGCACTGCGGTGAGTGCTGT\t~~~~~~~"
## [7] "GCCTTTTACAGTTCGTACT\t0\tchr12\t170820\t37\t19M\t*\t0\t0\tGCCTTTTACAGTTCGTACT\t~~~~~~~"
## [8] "GTCATGCCCCCTCAGCCAG\t0\tchr12\t170703\t37\t19M\t*\t0\t0\tGTCATGCCCCCTCAGCCAG\t~~~~~~~"
## [9] "TCGGCTCTCACCGTGTCCG\t0\tchr12\t170646\t37\t19M\t*\t0\t0\tTCGGCTCTCACCGTGTCCG\t~~~~~~~"

Aligment with `bwa_mem`

The bwa_mem function works similar to the bwa_aln function, except that it does not produce intermediate .sai files; it outputs a SAM file directly:

fastq <- system.file(package="Rbwa",
                     "fastq/sequences.fastq")
bwa_mem(index_prefix=index_prefix,
        fastq_files=fastq,
        sam_file=file.path(dir, "output.sam"))

strtrim(readLines(file.path(dir, "output.sam")), 65)

## [1] "@SQ\tSN:chr12\tLN:171330"                                                               
## [2] "@PG\tID:bwa\tPN:bwa\tVN:0.7.17-r1198-dirty\tCL:/tmp/RtmpRt1Iia/Rinst95016"              
## [3] "ACATCAGAAAGAGCGGCAG\t4\t*\t0\t0\t*\t*\t0\t0\tACATCAGAAAGAGCGGCAG\t~~~~~~~~~~~~~~~~~~~\t"
## [4] "CAACCCAGCCCCCCTCCAA\t4\t*\t0\t0\t*\t*\t0\t0\tCAACCCAGCCCCCCTCCAA\t~~~~~~~~~~~~~~~~~~~\t"
## [5] "CCTGTGATCCACGGAGGCT\t4\t*\t0\t0\t*\t*\t0\t0\tCCTGTGATCCACGGAGGCT\t~~~~~~~~~~~~~~~~~~~\t"
## [6] "GCACTGCGGTGAGTGCTGT\t4\t*\t0\t0\t*\t*\t0\t0\tGCACTGCGGTGAGTGCTGT\t~~~~~~~~~~~~~~~~~~~\t"
## [7] "GCCTTTTACAGTTCGTACT\t4\t*\t0\t0\t*\t*\t0\t0\tGCCTTTTACAGTTCGTACT\t~~~~~~~~~~~~~~~~~~~\t"
## [8] "GTCATGCCCCCTCAGCCAG\t4\t*\t0\t0\t*\t*\t0\t0\tGTCATGCCCCCTCAGCCAG\t~~~~~~~~~~~~~~~~~~~\t"
## [9] "TCGGCTCTCACCGTGTCCG\t4\t*\t0\t0\t*\t*\t0\t0\tTCGGCTCTCACCGTGTCCG\t~~~~~~~~~~~~~~~~~~~\t"

Session info

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Rbwa_1.11.0      BiocStyle_2.35.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       R6_2.5.1            fastmap_1.2.0      
##  [4] xfun_0.49           maketools_1.3.1     cachem_1.1.0       
##  [7] knitr_1.49          htmltools_0.5.8.1   rmarkdown_2.29     
## [10] buildtools_1.0.0    lifecycle_1.0.4     cli_3.6.3          
## [13] sass_0.4.9          jquerylib_0.1.4     compiler_4.4.2     
## [16] sys_3.4.3           tools_4.4.2         evaluate_1.0.1     
## [19] bslib_0.8.0         yaml_2.3.10         BiocManager_1.30.25
## [22] jsonlite_1.8.9      rlang_1.1.4

References

Li, Heng. 2013. “Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM.” arXiv Preprint arXiv:1303.3997.

Li, Heng, and Richard Durbin. 2009. “Fast and Accurate Short Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 25 (14): 1754–60.

An introduction to Rbwa