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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/bowtie2-test
%%DATADIR%%/scripts/bowtie2-hbb.sh
%%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%%/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/combined_reads.bam
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/conversion_utilities.sh
%%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
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