PopAlu

PopAlu detects polymorphic Alu elements in high-throughput sequencing data at the population scale.

Dependencies

This program requires:

• SeqAn library to be installed (http://www.seqan.de/)

Addtionally, you might want to install:

• boost library (http://www.boost.org/)
• googletest framework (https://code.google.com/p/googletest/)

Modify the path of library at file 'Makefile.vars'

B_LIB = path_of_boost_lib
G_LIB = path_of_gtest_lib

Compiling the program

make OD=opt3 opt3/alu_usage
make OD=opt3 opt3/build_dist
make OD=opt3 opt3/alu_delete
make OD=opt3 opt3/alu_insert
make OD=opt3 opt3/unittest_insert

Running the program

opt3/alu_usage build_dist
opt3/alu_usage alu_delete
opt3/alu_usage alu_insert

Reference

Please cite:

Qian Y, Kehr B, Halldórsson BV. (2015) PopAlu: population-scale discovery of Alu polymorphisms. PeerJ PrePrints 3:e1430

https://peerj.com/preprints/1174/