bin/bowtie2
bin/bowtie2-align-l
bin/bowtie2-align-s
bin/bowtie2-build
bin/bowtie2-build-l
bin/bowtie2-build-s
bin/bowtie2-inspect
bin/bowtie2-inspect-l
bin/bowtie2-inspect-s
bin/scripts/bowtie2-hbb.sh
bin/scripts/convert_quals.pl
bin/scripts/gen_2b_occ_lookup.pl
bin/scripts/gen_occ_lookup.pl
bin/scripts/gen_solqual_lookup.pl
bin/scripts/infer_fraglen.pl
bin/scripts/make_a_thaliana_tair.sh
bin/scripts/make_b_taurus_UMD3.sh
bin/scripts/make_c_elegans.sh
bin/scripts/make_canFam2.sh
bin/scripts/make_d_melanogaster.sh
bin/scripts/make_e_coli.sh
bin/scripts/make_h_sapiens_ncbi36.sh
bin/scripts/make_h_sapiens_ncbi37.sh
bin/scripts/make_hg18.sh
bin/scripts/make_hg19.sh
bin/scripts/make_m_musculus_ncbi37.sh
bin/scripts/make_mm10.sh
bin/scripts/make_mm9.sh
bin/scripts/make_rn4.sh
bin/scripts/make_s_cerevisiae.sh
bin/scripts/sa.py
bin/scripts/sim/AlignmentCheck.pm
bin/scripts/sim/DNA.pm
bin/scripts/sim/Mutate.pm
bin/scripts/sim/RandDNA.pm
bin/scripts/sim/SampleRead.pm
bin/scripts/sim/Sim.pm
bin/scripts/sim/Test.pm
bin/scripts/sim/contrib/ForkManager.pm
bin/scripts/sim/run.pl
bin/scripts/sim/run.sh
bin/scripts/sim/unit.sh
bin/scripts/test/.gitignore
bin/scripts/test/DNA.pm
bin/scripts/test/README.md
bin/scripts/test/benchmark/benchmarks.py
bin/scripts/test/benchmark/data/conf/acc.json
bin/scripts/test/benchmark/data/conf/seta.bench
bin/scripts/test/benchmark/data/conf/speed.json
bin/scripts/test/benchmark/run.py
bin/scripts/test/benchmark/samreader.py
bin/scripts/test/big_data/reads/human_reads.fa
bin/scripts/test/big_data/reads/mouse_reads.fa
bin/scripts/test/bt2face.py
bin/scripts/test/btdata.py
bin/scripts/test/dataface.py
bin/scripts/test/large_idx.py
bin/scripts/test/regressions.py
bin/scripts/test/simple_tests.pl
bin/scripts/test/simple_tests.sh