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 %%DATADIR%%/scripts/convert_quals.pl %%DATADIR%%/scripts/gen_2b_occ_lookup.pl %%DATADIR%%/scripts/gen_occ_lookup.pl %%DATADIR%%/scripts/gen_solqual_lookup.pl %%DATADIR%%/scripts/infer_fraglen.pl %%DATADIR%%/scripts/make_a_thaliana_tair.sh %%DATADIR%%/scripts/make_b_taurus_UMD3.sh %%DATADIR%%/scripts/make_c_elegans.sh %%DATADIR%%/scripts/make_canFam2.sh %%DATADIR%%/scripts/make_d_melanogaster.sh %%DATADIR%%/scripts/make_e_coli.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh %%DATADIR%%/scripts/make_hg18.sh %%DATADIR%%/scripts/make_hg19.sh %%DATADIR%%/scripts/make_m_musculus_ncbi37.sh %%DATADIR%%/scripts/make_mm10.sh %%DATADIR%%/scripts/make_mm9.sh %%DATADIR%%/scripts/make_rn4.sh %%DATADIR%%/scripts/make_s_cerevisiae.sh %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/images/bowtie_logo.png %%PORTDOCS%%%%DOCSDIR%%/images/osi-certified.gif %%PORTDOCS%%%%DOCSDIR%%/images/sflogo.png %%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png %%PORTDOCS%%%%DOCSDIR%%/manual.html %%PORTDOCS%%%%DOCSDIR%%/release.txt %%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl %%PORTDOCS%%%%DOCSDIR%%/style.css %%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml %%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi %%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi %%PORTDOCS%%%%DOCSDIR%%/website/index.html %%PORTDOCS%%%%DOCSDIR%%/website/index.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi %%PORTDOCS%%%%DOCSDIR%%/website/news.shtml %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml %%PORTDOCS%%%%DOCSDIR%%/website/push.sh %%PORTDOCS%%%%DOCSDIR%%/website/push_images.sh %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.3.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/simulate.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reference/lambda_virus.fa