GitHub - tjni/bowtie: An ultrafast memory-efficient short read aligner

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An ultrafast memory-efficient short read aligner

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Name		Name	Last commit message	Last commit date
Latest commit History 2,221 Commits
.github/workflows		.github/workflows
doc		doc
genomes		genomes
indexes		indexes
reads		reads
scripts		scripts
.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.h		aligner.h
aligner_0mm.h		aligner_0mm.h
aligner_1mm.h		aligner_1mm.h
aligner_23mm.h		aligner_23mm.h
aligner_metrics.h		aligner_metrics.h
aligner_seed_mm.h		aligner_seed_mm.h
alphabet.cpp		alphabet.cpp
alphabet.h		alphabet.h
assert_helpers.h		assert_helpers.h
binary_sa_search.h		binary_sa_search.h
bitpack.h		bitpack.h
bitset.h		bitset.h
blockwise_sa.h		blockwise_sa.h
bowtie		bowtie
bowtie-build		bowtie-build
bowtie-inspect		bowtie-inspect
bowtie_build_main.cpp		bowtie_build_main.cpp
bowtie_inspect.cpp		bowtie_inspect.cpp
bowtie_main.cpp		bowtie_main.cpp
bt2_locks.cpp		bt2_locks.cpp
bt2_locks.h		bt2_locks.h
btypes.h		btypes.h
ccnt_lut.cpp		ccnt_lut.cpp
chaincat.cpp		chaincat.cpp
cpu_numa_info.cpp		cpu_numa_info.cpp
cpu_numa_info.h		cpu_numa_info.h
diff_sample.h		diff_sample.h
ds.h		ds.h
ebwt.cpp		ebwt.cpp
ebwt.h		ebwt.h
ebwt_build.cpp		ebwt_build.cpp
ebwt_search.cpp		ebwt_search.cpp
ebwt_search.h		ebwt_search.h
ebwt_search_backtrack.h		ebwt_search_backtrack.h
ebwt_search_util.cpp		ebwt_search_util.cpp
ebwt_search_util.h		ebwt_search_util.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
hit.cpp		hit.cpp
hit.h		hit.h
hit_set.cpp		hit_set.cpp
hit_set.h		hit_set.h
log.cpp		log.cpp
log.h		log.h
ls.cpp		ls.cpp
ls.h		ls.h
mem_ids.h		mem_ids.h
mm.h		mm.h
multikey_qsort.h		multikey_qsort.h
pat.cpp		pat.cpp
pat.h		pat.h
pool.h		pool.h
processor_support.h		processor_support.h
qual.cpp		qual.cpp
qual.h		qual.h
random_source.h		random_source.h
random_test.cpp		random_test.cpp
range.h		range.h
range_cache.h		range_cache.h
range_chaser.h		range_chaser.h
range_source.h		range_source.h
read.h		read.h
ref_aligner.cpp		ref_aligner.cpp
ref_aligner.h		ref_aligner.h
ref_read.cpp		ref_read.cpp
ref_read.h		ref_read.h
reference.h		reference.h
row_chaser.h		row_chaser.h
sam.cpp		sam.cpp
sam.h		sam.h
search_1mm_phase1.c		search_1mm_phase1.c
search_1mm_phase2.c		search_1mm_phase2.c
search_23mm_phase1.c		search_23mm_phase1.c
search_23mm_phase2.c		search_23mm_phase2.c
search_23mm_phase3.c		search_23mm_phase3.c
search_exact.c		search_exact.c
search_globals.h		search_globals.h
search_seeded_phase1.c		search_seeded_phase1.c
search_seeded_phase2.c		search_seeded_phase2.c

Repository files navigation

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

 - See AUTHORS for information about who wrote Bowtie and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie.
 - See NEWS for information about changes in this and previous versions
   of Bowtie.
 - See TUTORIAL for a quick example to get you started with Bowtie.