This is full code part of master thesis for Faculty of Electrical Engineering and Computing. Goal was to develop method for mapping bisulfite-treated sequencing reads to a genome using some of already existing mapping tools. The work is based on Accel-align tool: https://github.com/raja-appuswamy/accel-align-release
Since BisulfiteAligner uses Accel-align under-the-hood, there is TBB dependency
- source: https://github.com/01org/tbb/releases/tag/2019_U5
- libtbb-dev package
- clone (git clone --recursive https://github.com/skosier/diplomski-fer)
- Build it:
make
It's mandatory to build the index before alignment. Options:
-l INT the length of k-mers [32]
Example:
path-to-bisulfite-aligner/bsfindex -l 32 path-to-ref/ref.fna
It will generate two indices aside the reference genome as path-to-ref/ref.fna.ct_hash and path-to-ref/ref.fna.ga_hash.
When the alignment is triggered, the index will be loaded in memory automatically.
Options:
-t INT number of cpu threads to use [1].
-l INT length of seed [32].
-o name of output file to use.
-x alignment-free.
-w use WFA for extension. It's using KSW by default.
-p the maximum distance allowed between the paired-end reads [1000].
-d disable embedding, extend all candidates from seeding (this mode is super slow, only for benchmark).
Note: maximum read length and read name length supported are 512.
path-to-bisulfite-aligner/bsfalign options ref.fna read1.fastq read2.fastq
Example:
path-to-bisulfite-align/bsfalign -l 32 -t 4 -o output-path/out.sam \
path-to-ref/ref.fna input-path/read1.fastq input-path/read2.fastq
path-to-bisulfite-aligner/bsfalign options ref.fna read.fastq
Example:
path-to-bisulfite-aligner/bsfalign -l 32 -t 4 -o output-path/out.sam \
path-to-ref/ref.fna input-path/read.fastq
Paper about Accel-align can be found here https://doi.org/10.1186/s12859-021-04162-z :
Yan, Y., Chaturvedi, N. & Appuswamy, R. Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method. BMC Bioinformatics 22, 257 (2021).