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A fast and sensitive gapped read aligner

GPL-3.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 2,033 Commits
doc		doc
example		example
scripts		scripts
third_party		third_party
.gitignore		.gitignore
.travis.yml		.travis.yml
AUTHORS		AUTHORS
LICENSE		LICENSE
MANUAL		MANUAL
MANUAL.markdown		MANUAL.markdown
Makefile		Makefile
NEWS		NEWS
README		README
TUTORIAL		TUTORIAL
VERSION		VERSION
aligner_bt.cpp		aligner_bt.cpp
aligner_bt.h		aligner_bt.h
aligner_cache.cpp		aligner_cache.cpp
aligner_cache.h		aligner_cache.h
aligner_driver.cpp		aligner_driver.cpp
aligner_driver.h		aligner_driver.h
aligner_metrics.h		aligner_metrics.h
aligner_report.h		aligner_report.h
aligner_result.cpp		aligner_result.cpp
aligner_result.h		aligner_result.h
aligner_seed.cpp		aligner_seed.cpp
aligner_seed.h		aligner_seed.h
aligner_seed2.cpp		aligner_seed2.cpp
aligner_seed2.h		aligner_seed2.h
aligner_seed_policy.cpp		aligner_seed_policy.cpp
aligner_seed_policy.h		aligner_seed_policy.h
aligner_sw.cpp		aligner_sw.cpp
aligner_sw.h		aligner_sw.h
aligner_sw_common.h		aligner_sw_common.h
aligner_sw_driver.cpp		aligner_sw_driver.cpp
aligner_sw_driver.h		aligner_sw_driver.h
aligner_sw_nuc.h		aligner_sw_nuc.h
aligner_swsse.cpp		aligner_swsse.cpp
aligner_swsse.h		aligner_swsse.h
aligner_swsse_ee_i16.cpp		aligner_swsse_ee_i16.cpp
aligner_swsse_ee_u8.cpp		aligner_swsse_ee_u8.cpp
aligner_swsse_loc_i16.cpp		aligner_swsse_loc_i16.cpp
aligner_swsse_loc_u8.cpp		aligner_swsse_loc_u8.cpp
aln_sink.cpp		aln_sink.cpp
aln_sink.h		aln_sink.h
alphabet.cpp		alphabet.cpp
alphabet.h		alphabet.h
assert_helpers.h		assert_helpers.h
banded.cpp		banded.cpp
banded.h		banded.h
binary_sa_search.h		binary_sa_search.h
bitpack.h		bitpack.h
blockwise_sa.h		blockwise_sa.h
bowtie2		bowtie2
bowtie2-build		bowtie2-build
bowtie2-inspect		bowtie2-inspect
bowtie_build_main.cpp		bowtie_build_main.cpp
bowtie_main.cpp		bowtie_main.cpp
bt2_build.cpp		bt2_build.cpp
bt2_dp.cpp		bt2_dp.cpp
bt2_idx.cpp		bt2_idx.cpp
bt2_idx.h		bt2_idx.h
bt2_inspect.cpp		bt2_inspect.cpp
bt2_io.cpp		bt2_io.cpp
bt2_search.cpp		bt2_search.cpp
bt2_search.h		bt2_search.h
bt2_util.cpp		bt2_util.cpp
btypes.h		btypes.h
ccnt_lut.cpp		ccnt_lut.cpp
cpu_numa_info.cpp		cpu_numa_info.cpp
cpu_numa_info.h		cpu_numa_info.h
diff_sample.cpp		diff_sample.cpp
diff_sample.h		diff_sample.h
dp_framer.cpp		dp_framer.cpp
dp_framer.h		dp_framer.h
ds.cpp		ds.cpp
ds.h		ds.h
edit.cpp		edit.cpp
edit.h		edit.h
endian_swap.h		endian_swap.h
fast_mutex.h		fast_mutex.h
filebuf.h		filebuf.h
formats.h		formats.h
group_walk.cpp		group_walk.cpp
group_walk.h		group_walk.h
ival_list.cpp		ival_list.cpp
ival_list.h		ival_list.h
limit.cpp		limit.cpp
limit.h		limit.h
ls.cpp		ls.cpp
ls.h		ls.h
mask.cpp		mask.cpp
mask.h		mask.h
mem_ids.h		mem_ids.h
mm.h		mm.h
multikey_qsort.cpp		multikey_qsort.cpp
multikey_qsort.h		multikey_qsort.h
opts.h		opts.h
outq.cpp		outq.cpp
outq.h		outq.h

Repository files navigation

Bowtie 2: http://bowtie-bio.sf.net/bowtie2

 - See AUTHORS for information about who wrote Bowtie 2 and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie 2.
 - See NEWS for information about changes in this and previous versions
   of Bowtie 2.