GitHub - iamjinholee/bwa: Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

BWA-MEM ON GPU

GPU implementation of BWA-MEM.

Create a symlink from the cuda installation to /usr/local/cuda (CUDA installer should have alrady done this)

make

Same CLI usage as BWA-MEM

Name		Name	Last commit message	Last commit date
Latest commit History 974 Commits
bwakit		bwakit
cuda		cuda
kmers_index		kmers_index
.gitignore		.gitignore
.travis.yml		.travis.yml
COPYING		COPYING
ChangeLog		ChangeLog
Makefile		Makefile
NEWS.md		NEWS.md
QSufSort.c		QSufSort.c
QSufSort.h		QSufSort.h
README-alt.md		README-alt.md
README.md		README.md
bamlite.c		bamlite.c
bamlite.h		bamlite.h
bntseq.c		bntseq.c
bntseq.h		bntseq.h
bwa.1		bwa.1
bwa.c		bwa.c
bwa.h		bwa.h
bwamem.c		bwamem.c
bwamem.h		bwamem.h
bwamem_extra.c		bwamem_extra.c
bwamem_pair.c		bwamem_pair.c
bwape.c		bwape.c
bwase.c		bwase.c
bwase.h		bwase.h
bwaseqio.c		bwaseqio.c
bwashm.c		bwashm.c
bwt.c		bwt.c
bwt.h		bwt.h
bwt_gen.c		bwt_gen.c
bwt_lite.c		bwt_lite.c
bwt_lite.h		bwt_lite.h
bwtaln.c		bwtaln.c
bwtaln.h		bwtaln.h
bwtgap.c		bwtgap.c
bwtgap.h		bwtgap.h
bwtindex.c		bwtindex.c
bwtsw2.h		bwtsw2.h
bwtsw2_aux.c		bwtsw2_aux.c
bwtsw2_chain.c		bwtsw2_chain.c
bwtsw2_core.c		bwtsw2_core.c
bwtsw2_main.c		bwtsw2_main.c
bwtsw2_pair.c		bwtsw2_pair.c
example.c		example.c
fastmap.c		fastmap.c
is.c		is.c
kbtree.h		kbtree.h
khash.h		khash.h
kopen.c		kopen.c
kseq.h		kseq.h
ksort.h		ksort.h
kstring.c		kstring.c
kstring.h		kstring.h
ksw.c		ksw.c
ksw.h		ksw.h
kthread.c		kthread.c
kvec.h		kvec.h
main.c		main.c
malloc_wrap.c		malloc_wrap.c
malloc_wrap.h		malloc_wrap.h
maxk.c		maxk.c
pemerge.c		pemerge.c
qualfa2fq.pl		qualfa2fq.pl
rle.c		rle.c
rle.h		rle.h
rope.c		rope.c
rope.h		rope.h
utils.c		utils.c
utils.h		utils.h
xa2multi.pl		xa2multi.pl