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Last pushed: a year ago
Short Description
Smith-Waterman alignment for immunoglobulins
Full Description


Smith-Waterman alignment for immunoglobulin sequences.


This is a C++ implementation of the vdjalign align-fastq command in ighutil. This implementation uses the Smith-Waterman (SW) alignment algorithm, a simple but effective way to align DNA sequences, as in ighutil.

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Running the alignment

Clone the repository and run scons from the ig-sw/src/ig_align/ directory.

To run the sw-alignment, run ./ig-sw with the appropriate arguments in the same directory or add a path to the executable.


./ig-sw -p test_data/ query_file.fasta output_file.sam


ig-sw uses the tclap command line interface.

Flag Description
(none) The path to the query file
(none) The path to the output file
-p --vdj-dir Directory from which to read germline genes (ending with /)
Flag Description Default Value
-l --locus Locus to align reads against (options: IGH, IGK, IGL, DJ) IGH
-m --match Match score 2
-u --mismatch Mismatch score 2
-o --gap-open Gap opening penalty 3
-e --gap-extend Gap extension penalty 1
-d --max-drop Max drop 1000
-s --min-score Min score 0
-b --bandwidth Bandwidth 150
-j --threads Number of threads 1


ig_align_main.cpp takes in a DNA sequence in FASTQ format, does alignment, and outputs a file in SAM format.

ig_align_main.cpp calls the ig_align_reads function of ig_align.c which heavily utilizes the klib library.

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