owtie used to this tool than a tool to speed fast and good results

bowtie-0.12.7
.............\scripts
.............\.......\build_test.sh
.............\.......\make_a_thaliana_tair.sh
.............\.......\make_b_taurus_UMD3.sh
.............\.......\make_canFam2.sh
.............\.......\make_c_elegans_ws200.sh
.............\.......\make_d_melanogaster_fb5_22.sh
.............\.......\make_e_coli.sh
.............\.......\make_galGal3.sh
.............\.......\make_hg18.sh
.............\.......\make_hg19.sh
.............\.......\make_h_sapiens_ncbi36.sh
.............\.......\make_h_sapiens_ncbi37.sh
.............\.......\make_mm8.sh
.............\.......\make_mm9.sh
.............\.......\make_m_musculus_ncbi37.sh
.............\.......\make_rn4.sh
.............\.......\make_s_cerevisiae.sh
.............\.......\random_bowtie_tests_p.sh
.............\.......\random_bowtie_tests.sh
.............\.......\best_verify.pl
.............\.......\bs_mapability.pl
.............\.......\colorize_fasta.pl
.............\.......\colorize_fastq.pl
.............\.......\convert_quals.pl
.............\.......\fastq_to_tabbed.pl
.............\.......\gen_2b_occ_lookup.pl
.............\.......\gen_dnamasks2colormask.pl
.............\.......\gen_occ_lookup.pl
.............\.......\gen_solqual_lookup.pl
.............\.......\mapability.pl
.............\.......\pe_verify.pl
.............\.......\random_bowtie_tests.pl
.............\.......\reconcile_alignments_pe.pl
.............\.......\reconcile_alignments.pl
.............\.......\test.pl
.............\indexes
.............\.......\e_coli.1.ebwt
.............\.......\e_coli.2.ebwt
.............\.......\e_coli.3.ebwt
.............\.......\e_coli.4.ebwt
.............\.......\e_coli.README
.............\.......\e_coli.rev.1.ebwt
.............\.......\e_coli.rev.2.ebwt
.............\genomes
.............\.......\NC_008253.fna
.............\reads
.............\.....\e_coli_1000.fa
.............\.....\e_coli_1000.fq
.............\.....\e_coli_1000.raw
.............\.....\e_coli_1000_1.fa
.............\.....\e_coli_1000_1.fq
.............\.....\e_coli_1000_2.fa
.............\.....\e_coli_1000_2.fq
.............\.....\e_coli_10000snp.fa
.............\.....\e_coli_10000snp.fq
.............\doc
.............\...\manual.html
.............\...\README
.............\...\style.css
.............\AUTHORS
.............\COPYING
.............\NEWS
.............\MANUAL
.............\MANUAL.markdown
.............\TUTORIAL
.............\VERSION
.............\bowtie-build
.............\bowtie
.............\bowtie-inspect
.............\bowtie-build-debug
.............\bowtie-debug
.............\bowtie-inspect-debug

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