/bowtie2

A fast and sensitive gapped read aligner
  1. C++ 81.4%
  2. Perl 14.0%
  3. Python 1.5%
  4. Shell 1.0%
  5. C 1.0%
  6. Makefile 0.5%
  7. Other 0.6%
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doc
example
scripts
third_party
.gitignore
.travis.yml
AUTHORS
LICENSE
MANUAL
MANUAL.markdown
Makefile
NEWS
README
TUTORIAL
VERSION
aligner_bt.cpp
aligner_bt.h
aligner_cache.cpp
aligner_cache.h
aligner_driver.cpp
aligner_driver.h
aligner_metrics.h
aligner_report.h
aligner_result.cpp
aligner_result.h
aligner_seed.cpp
aligner_seed.h
aligner_seed2.cpp
aligner_seed2.h
aligner_seed_policy.cpp
aligner_seed_policy.h
aligner_sw.cpp
aligner_sw.h
aligner_sw_common.h
aligner_sw_driver.cpp
aligner_sw_driver.h
aligner_sw_nuc.h
aligner_swsse.cpp
aligner_swsse.h
aligner_swsse_ee_i16.cpp
aligner_swsse_ee_u8.cpp
aligner_swsse_loc_i16.cpp
aligner_swsse_loc_u8.cpp
aln_sink.cpp
aln_sink.h
alphabet.cpp
alphabet.h
assert_helpers.h
banded.cpp
banded.h
binary_sa_search.h
bitpack.h
blockwise_sa.h
bowtie2
bowtie2-build
bowtie2-inspect
bowtie_build_main.cpp
bowtie_main.cpp
bt2_build.cpp
bt2_dp.cpp
bt2_idx.cpp
bt2_idx.h
bt2_inspect.cpp
bt2_io.cpp
bt2_search.cpp
bt2_search.h
bt2_util.cpp
btypes.h
ccnt_lut.cpp
diff_sample.cpp
diff_sample.h
dp_framer.cpp
dp_framer.h
ds.cpp
ds.h
edit.cpp
edit.h
endian_swap.h
fast_mutex.h
filebuf.h
formats.h
group_walk.cpp
group_walk.h
hints.cpp
hints.h
ival_list.cpp
ival_list.h
limit.cpp
limit.h
ls.cpp
ls.h
mask.cpp
mask.h
mem_ids.h
mm.h
multikey_qsort.cpp
multikey_qsort.h
opts.h
outq.cpp
outq.h
pat.cpp
pat.h
pe.cpp
pe.h
presets.cpp
presets.h
processor_support.h
pthreadGC2.dll
qual.cpp
qual.h
random_source.cpp
random_source.h
random_util.cpp
random_util.h
read.h
read_qseq.cpp
ref_coord.cpp
ref_coord.h
ref_read.cpp
ref_read.h
reference.cpp
reference.h
sam.cpp
sam.h
scoring.cpp
scoring.h
search_globals.h
sequence_io.h
shmem.cpp
shmem.h
simple_func.cpp
simple_func.h
sse_util.cpp
sse_util.h
sstring.cpp
sstring.h
str_util.h
threading.h
timer.h
tinythread.cpp
tinythread.h
tokenize.h
unique.cpp
unique.h
util.h
word_io.h
zbox.h

README 

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.