TurboMap

A GPU-accelerated extension alignment engine for long-read sequencing that delivers high speed with near-lossless accuracy.

Build

make -j$(nproc) GPUARCH=sm_80

Optional flags:

./minimap2 -a -t $(nproc) --gpu --gpu-cfg gpu/gpu_config.json ref.mmi reads.fastq.gz > out.sam

MIT (see LICENSE.txt), inheriting from upstream minimap2.

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
cJSON		cJSON
gpu		gpu
.gitignore		.gitignore
LICENSE.txt		LICENSE.txt
Makefile		Makefile
README.md		README.md
align.c		align.c
bseq.c		bseq.c
bseq.h		bseq.h
diff.py		diff.py
esterr.c		esterr.c
example.c		example.c
format.c		format.c
hit.c		hit.c
index.c		index.c
kalloc.c		kalloc.c
kalloc.h		kalloc.h
kdq.h		kdq.h
ketopt.h		ketopt.h
khash.h		khash.h
krmq.h		krmq.h
kseq.h		kseq.h
ksort.h		ksort.h
ksw2.h		ksw2.h
ksw2_dispatch.c		ksw2_dispatch.c
ksw2_extd2_sse.c		ksw2_extd2_sse.c
ksw2_exts2_sse.c		ksw2_exts2_sse.c
ksw2_extz2_sse.c		ksw2_extz2_sse.c
ksw2_ll_sse.c		ksw2_ll_sse.c
kthread.c		kthread.c
kthread.h		kthread.h
kvec.h		kvec.h
lchain.c		lchain.c
main.c		main.c
map.c		map.c
minimap.h		minimap.h
misc.c		misc.c
mmpriv.h		mmpriv.h
options.c		options.c
pe.c		pe.c
sdust.c		sdust.c
sdust.h		sdust.h
seed.c		seed.c
sketch.c		sketch.c
splitidx.c		splitidx.c