drwxr-xr-x root/root usr/ drwxr-xr-x root/root usr/bin/ -rwxr-xr-x root/root usr/bin/bowtie2 -rwxr-xr-x root/root usr/bin/bowtie2-align-l -rwxr-xr-x root/root usr/bin/bowtie2-align-s -rwxr-xr-x root/root usr/bin/bowtie2-build -rwxr-xr-x root/root usr/bin/bowtie2-build-l -rwxr-xr-x root/root usr/bin/bowtie2-build-s -rwxr-xr-x root/root usr/bin/bowtie2-inspect -rwxr-xr-x root/root usr/bin/bowtie2-inspect-l -rwxr-xr-x root/root usr/bin/bowtie2-inspect-s drwxr-xr-x root/root usr/share/ drwxr-xr-x root/root usr/share/bowtie2/ drwxrwxr-x root/root usr/share/bowtie2/example/ drwxrwxr-x root/root usr/share/bowtie2/example/index/ -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.1.bt2.gz -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.2.bt2.gz -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.3.bt2.gz -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.4.bt2.gz -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.rev.1.bt2.gz -rw-rw-r-- root/root usr/share/bowtie2/example/index/lambda_virus.rev.2.bt2.gz drwxrwxr-x root/root usr/share/bowtie2/example/reads/ -rw-rw-r-- root/root usr/share/bowtie2/example/reads/combined_reads.bam -rw-rw-r-- root/root usr/share/bowtie2/example/reads/conversion_utilities.sh -rw-rw-r-- root/root usr/share/bowtie2/example/reads/longreads.fq.gz -rw-rw-r-- root/root usr/share/bowtie2/example/reads/reads_1.fq.gz -rw-rw-r-- root/root usr/share/bowtie2/example/reads/reads_2.fq.gz -rw-rw-r-- root/root usr/share/bowtie2/example/reads/simulate.pl drwxrwxr-x root/root usr/share/bowtie2/example/reference/ -rw-rw-r-- root/root usr/share/bowtie2/example/reference/lambda_virus.fa drwxrwxr-x root/root usr/share/bowtie2/scripts/ -rwxrwxr-x root/root usr/share/bowtie2/scripts/bowtie2-hbb.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/convert_quals.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/gen_2b_occ_lookup.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/gen_occ_lookup.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/gen_solqual_lookup.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/infer_fraglen.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_a_thaliana_tair.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_b_taurus_UMD3.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_c_elegans.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_canFam2.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_d_melanogaster.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_e_coli.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_h_sapiens_ncbi36.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_h_sapiens_ncbi37.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_hg18.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_hg19.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_m_musculus_ncbi37.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_mm10.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_mm9.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_rn4.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/make_s_cerevisiae.sh -rwxrwxr-x root/root usr/share/bowtie2/scripts/sa.py drwxrwxr-x root/root usr/share/bowtie2/scripts/sim/ -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/AlignmentCheck.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/DNA.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/Mutate.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/RandDNA.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/SampleRead.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/Sim.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/Test.pm drwxrwxr-x root/root usr/share/bowtie2/scripts/sim/contrib/ -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/contrib/ForkManager.pm -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/run.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/sim/run.sh -rw-rw-r-- root/root usr/share/bowtie2/scripts/sim/unit.sh drwxrwxr-x root/root usr/share/bowtie2/scripts/test/ -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/.gitignore -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/DNA.pm drwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/ -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/benchmarks.py drwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/data/ drwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/data/conf/ -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/benchmark/data/conf/acc.json -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/benchmark/data/conf/seta.bench -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/benchmark/data/conf/speed.json -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/run.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/benchmark/samreader.py drwxrwxr-x root/root usr/share/bowtie2/scripts/test/big_data/ drwxrwxr-x root/root usr/share/bowtie2/scripts/test/big_data/reads/ -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/big_data/reads/human_reads.fa -rw-rw-r-- root/root usr/share/bowtie2/scripts/test/big_data/reads/mouse_reads.fa -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/bt2face.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/btdata.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/dataface.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/large_idx.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/regressions.py -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/simple_tests.pl -rwxrwxr-x root/root usr/share/bowtie2/scripts/test/simple_tests.sh