The R package ssw offers an R interface for SSW, a fast implementation of the Smith-Waterman algorithm for sequence alignment using SIMD, described in Zhao et al. (2013). The package is currently built on ssw-py.
A short read sequence:
read <- "ACGT"Exact alignment
Align the read against the reference sequence
(TTTTACGTCCCCC) and print the results:
read |> align("TTTTACGTCCCCC")CIGAR start index 4: 4M
optimal_score: 8
sub-optimal_score: 0
target_begin: 4 target_end: 7
query_begin: 0
query_end: 3
Target: 4 ACGT 7
||||
Query: 0 ACGT 3Get specific results, such as the alignment scores:
a <- read |> align("TTTTACGTCCCCC")
a$alignment$optimal_score[1] 8
a$alignment$sub_optimal_score[1] 0Deletion
read |> align("TTTTACAGTCCCCC")CIGAR start index 4: 2M1D2M
optimal_score: 5
sub-optimal_score: 0
target_begin: 4 target_end: 8
query_begin: 0
query_end: 3
Target: 4 ACAGT 8
||*||
Query: 0 AC-GT 3Insertion with gap open
read |> align("TTTTACTCCCCC", gap_open = 3)CIGAR start index 4: 2M
optimal_score: 4
sub-optimal_score: 0
target_begin: 4 target_end: 5
query_begin: 0
query_end: 1
Target: 4 AC 5
||
Query: 0 AC 1Insertion with no gap open penalty
read |> align("TTTTACTCCCCC", gap_open = 0)CIGAR start index 4: 2M1I1M
optimal_score: 6
sub-optimal_score: 0
target_begin: 4 target_end: 6
query_begin: 0
query_end: 3
Target: 4 AC-T 6
||*|
Query: 0 ACGT 3Specify start index
a <- align("ACTG", "ACTCACTG", start_idx = 4)
aCIGAR start index 0: 4M
optimal_score: 8
sub-optimal_score: 0
target_begin: 0 target_end: 3
query_begin: 0
query_end: 3
Target: 0 ACTC 3
|||*
Query: 0 ACTG 3Print the results from position 4:
a |> print(start_idx = 4)CIGAR start index 0: 4M
optimal_score: 8
sub-optimal_score: 0
target_begin: 0 target_end: 3
query_begin: 0
query_end: 3
Target: 0 ACTG 3
||||
Query: 0 ACTG 3Forced alignment
Enforce no gaps by increasing the penalty:
a <- force_align("ACTG", "TTTTCTGCCCCCACG")
aThe results are truncated:
CIGAR start index 4: 3M
optimal_score: 6
sub-optimal_score: 0
target_begin: 4 target_end: 6
query_begin: 1
query_end: 3
Target: 4 CTG 6
|||
Query: 1 CTG 3Use formatter() to avoid the truncation:
b <- a |> formatter()
b[[1]]
[1] "TTTTCTGCCCCCACG"
[[2]]
[1] " ACTG"Or pretty-print the formatted results directly:
a |> formatter(print = TRUE)TTTTCTGCCCCCACG
ACTGAcknowledgements
ssw-r is built upon the work of two outstanding projects:
- SSW - Original C implementation. Author: Mengyao Zhao
- ssw-py - Python binding for SSW. Author: Nick Conway
We extend our sincere gratitude to Mengyao Zhao for developing the original SSW library and to Nick Conway for maintaining the ssw-py package. Their work forms the foundation of ssw-r. While ssw-r does not directly incorporate code from these projects, it serves as an R interface to their functionality. We encourage users to visit the original repositories for more information about the underlying implementation and to consider citing these works in publications that use ssw-r.