LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads

LongAGE is a memory-efficient implementation of AGE (https://github.com/abyzovlab/AGE). Its memory footprint is less than hundreds of megabytes, while it is at most four times slower than AGE in terms of running time.

The tool refines the resolution and standardization of structural variant (SV) breakpoints in highly repetitive regions at a single base pair. It is capable of refining read alignment once a read has been heuristically mapped to a particular genomic location that is expected to contain an SV.

Compilation

git clone https://github.com/Coaxecva/LongAGE.git
cd LongAGE
make

Running

./long_age_align file1.fa file2.fa

Help

./long_age_align

Examples

# INDEL mode (default)
./long_age_align part_chr19.fa seq_first.fa 
./long_age_align -indel part_chr19.fa seq_first.fa 
# TDUP mode
./long_age_align -tdup part_chr19.fa seq_second.fa

Bugs

Feel free to report any bugs that you find on GitHub: https://github.com/Coaxecva/LongAGE/issues

License

Released under MIT licence.