├── CHANGELOG ├── LICENSE ├── README.md ├── docs ├── MANUAL.html ├── MANUAL.markdown ├── Makefile ├── bar-bg.png ├── head.html ├── kraken.css └── top.html ├── install_kraken.sh ├── scripts ├── add_to_library.sh ├── build_kraken_db.sh ├── check_for_jellyfish.sh ├── clean_db.sh ├── convert_gb_to_fa.pl ├── cp_into_tempfile.pl ├── download_genomic_library.sh ├── download_taxonomy.sh ├── kraken ├── kraken-build ├── kraken-filter ├── kraken-mpa-report ├── kraken-report ├── kraken-translate ├── krakenlib.pm ├── lookup_accession_numbers.pl ├── read_merger.pl ├── report_gi_numbers.pl ├── rsync_from_ncbi.pl ├── scan_fasta_file.pl ├── shrink_db.sh ├── standard_installation.sh ├── upgrade_db.sh └── verify_gi_numbers.pl └── src ├── Makefile ├── classify.cpp ├── db_shrink.cpp ├── db_sort.cpp ├── kmer_estimator.cpp ├── kraken_headers.hpp ├── krakendb.cpp ├── krakendb.hpp ├── krakenutil.cpp ├── krakenutil.hpp ├── make_seqid_to_taxid_map.cpp ├── quickfile.cpp ├── quickfile.hpp ├── seqreader.cpp ├── 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