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

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 1,767 Commits
SeqAn-1.1		SeqAn-1.1
doc		doc
genomes		genomes
indexes		indexes
reads		reads
scripts		scripts
third_party		third_party
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
annot.cpp		annot.cpp
annot.h		annot.h
assert_helpers.h		assert_helpers.h
auto_array.h		auto_array.h
binary_sa_search.h		binary_sa_search.h
bitpack.h		bitpack.h
bitset.h		bitset.h
blockwise_sa.h		blockwise_sa.h
bowtie_build_main.cpp		bowtie_build_main.cpp
bowtie_inspect.cpp		bowtie_inspect.cpp
bowtie_main.cpp		bowtie_main.cpp
ccnt_lut.cpp		ccnt_lut.cpp
chaincat.cpp		chaincat.cpp
color.cpp		color.cpp
color.h		color.h
color_dec.cpp		color_dec.cpp
color_dec.h		color_dec.h
diff_sample.h		diff_sample.h
ebwt.cpp		ebwt.cpp
ebwt.h		ebwt.h
ebwt_build.cpp		ebwt_build.cpp
ebwt_search.cpp		ebwt_search.cpp
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
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
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
refmap.cpp		refmap.cpp
refmap.h		refmap.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
search_seeded_phase3.c		search_seeded_phase3.c
search_seeded_phase4.c		search_seeded_phase4.c
sequence_io.h		sequence_io.h
shmem.cpp		shmem.cpp
shmem.h		shmem.h
str_util.h		str_util.h

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.