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required_file_list.txt
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setup.py
doc/citations.rst
doc/HOW-TO.rst
doc/Manual.rst
img/blocks_dark_tiny.png
img/name.png
src/abundance.py
src/annotate.py
src/assemble.py
src/calcdist.py
src/classify.py
src/fannotate.py
src/findorfs.py
src/findreps.py
src/findscforfs.py
src/initPipeline.py
src/mapreads.py
src/postprocess.py
src/preprocess.py
src/propagate.py
src/runPipeline.py
src/scaffold.py
src/utils.py
Test/carsonella_pe_filt.fna
Test/carsonella_pe_filt.fq
Test/carsonella_reference.fna
Test/MA_test2.filt2.fna
Test/run_test.sh
Test/run_test2.sh
Test/run_test3.sh
Test/test.asm
Test/test1.fq
Test/test12.fq
Test/test2.fq
Test/test_amphora.sh
Test/test_bowtie2.sh
Test/test_ca.sh
Test/test_ca_fasta.sh
Test/test_create.sh
Test/test_fcp.sh
Test/test_filter_noninterleaved_fastq.sh
Test/test_metaphyler.sh
Test/test_metavelvet.sh
Test/test_minimus.sh
Test/test_missingfiles.sh
Test/test_newbler.sh
Test/test_phymm.sh
Test/test_soap.sh
Test/test_sparse.sh
Test/test_velvet.sh
Tutorial/metamos.jpg
Tutorial/example_html/abund.png
Tutorial/example_html/Abundance.html
Tutorial/example_html/Annotate.html
Tutorial/example_html/asmstats.out
Tutorial/example_html/bar-phylum.png
Tutorial/example_html/blocks_dark_tiny.png
Tutorial/example_html/ContigSizes.pdf
Tutorial/example_html/ContigSizes.png
Tutorial/example_html/ContigSizes2.pdf
Tutorial/example_html/ContigSizes2.png
Tutorial/example_html/covstats.out
Tutorial/example_html/functionalannotation.html
Tutorial/example_html/hist_contigs.pdf
Tutorial/example_html/hist_contigs.png
Tutorial/example_html/hist_ctgcvg.pdf
Tutorial/example_html/hist_ctgcvg.png
Tutorial/example_html/hist_orf.pdf
Tutorial/example_html/hist_orf.png
Tutorial/example_html/hist_scaffold.pdf
Tutorial/example_html/hist_scaffold.png
Tutorial/example_html/MapReads.html
Tutorial/example_html/name.png
Tutorial/example_html/ORFSizes.pdf
Tutorial/example_html/ORFSizes.png
Tutorial/example_html/phylum.classified
Tutorial/example_html/pipeline.commands
Tutorial/example_html/pipeline.summary
Tutorial/example_html/plot.tab
Tutorial/example_html/Preprocess.html
Tutorial/example_html/propagate.out.clusters
Tutorial/example_html/ScaffoldSizes.pdf
Tutorial/example_html/ScaffoldSizes.png
Tutorial/example_html/ScaffoldSizes2.pdf
Tutorial/example_html/ScaffoldSizes2.png
Tutorial/example_html/SCFORFSizes.pdf
Tutorial/example_html/SCFORFSizes.png
Tutorial/example_html/stats.out
Tutorial/example_html/style.css
Tutorial/example_html/summary.html
Tutorial/example_html/img/._hidden.png
Tutorial/example_html/img/._loading.gif
Tutorial/example_html/img/favicon.ico
Tutorial/example_html/img/hidden.png
Tutorial/example_html/img/loading.gif
Tutorial/example_html/src/krona-2.0.js
Utilities/config/454.linker.fasta
Utilities/config/asm.spec
Utilities/config/bambus.spec
Utilities/config/lr.tab
Utilities/config/markerstax.tab
Utilities/config/MetaGeneMark_v1.mod
Utilities/config/metaidba.spec
Utilities/config/metavelvet.spec
Utilities/config/newbler.spec
Utilities/config/soap.spec
Utilities/config/soapconfig.txt
Utilities/config/spades.spec
Utilities/config/SparseAssembler.spec
Utilities/config/updateftpcounter.sh
Utilities/cpp/Linux-x86_64/MetaVelvet/scripts/scriptEstimatedCovMulti.py
Utilities/cpp/Linux-x86_64/MetaVelvet/scripts/shuffleAndConvertSequences_fastq2fasta.py
Utilities/cpp/Linux-x86_64/MetaVelvet/scripts/shuffleSequences_fasta.pl
Utilities/cpp/Linux-x86_64/MetaVelvet/scripts/shuffleSequences_fastq.pl
Utilities/cpp/Linux-x86_64/velvet/Columbus_manual.pdf
Utilities/cpp/Linux-x86_64/velvet/CREDITS.txt
Utilities/cpp/Linux-x86_64/velvet/LICENSE.txt
Utilities/cpp/Linux-x86_64/velvet/Manual.pdf
Utilities/cpp/Linux-x86_64/velvet/README.txt
Utilities/cpp/Linux-x86_64/velvet/shuffleSequences_fasta.pl
Utilities/cpp/Linux-x86_64/velvet/shuffleSequences_fastq.pl
Utilities/cpp/Linux-x86_64/velvet-sc/CREDITS.txt
Utilities/cpp/Linux-x86_64/velvet-sc/CREDITS_velvetsc.txt
Utilities/cpp/Linux-x86_64/velvet-sc/LICENSE.txt
Utilities/cpp/Linux-x86_64/velvet-sc/LICENSE_velvetsc.txt
Utilities/cpp/Linux-x86_64/velvet-sc/Manual.pdf
Utilities/cpp/Linux-x86_64/velvet-sc/README.txt
Utilities/cpp/Linux-x86_64/velvet-sc/README_velvetsc.txt
Utilities/cpp/Linux-x86_64/velvet-sc/shuffleSequences_fasta.pl
Utilities/cpp/Linux-x86_64/velvet-sc/shuffleSequences_fastq.pl
Utilities/DB/class_key.tab
Utilities/DB/markers.fna
Utilities/DB/markers.missingGI.txt
Utilities/DB/markers.pfasta
Utilities/DB/markers.toGI.txt
Utilities/DB/mergedTaxonomy.tab
Utilities/DB/tax_key.tab
Utilities/java/buildBambusInput$1.class
Utilities/java/buildBambusInput$MappingInfo.class
Utilities/java/buildBambusInput.class
Utilities/java/buildBambusInput.java
Utilities/java/convert454GraphToCTL.class
Utilities/java/convert454GraphToCTL.java
Utilities/java/convertFastaAndQualToFastq.class
Utilities/java/convertFastaAndQualToFastq.java
Utilities/java/convertFastqToFasta.class
Utilities/java/convertFastqToFasta.java
Utilities/java/outputDefaultQuality.class
Utilities/java/outputDefaultQuality.java
Utilities/java/SizeFasta.class
Utilities/java/SizeFasta.java
Utilities/java/SubFile$Pair.class
Utilities/java/SubFile.class
Utilities/java/SubFile.java
Utilities/java/Utils$Pair.class
Utilities/java/Utils$ToProtein.class
Utilities/java/Utils$Translate.class
Utilities/java/Utils.class
Utilities/java/Utils.java
Utilities/javascript/Assemble.html
Utilities/javascript/FindORFS.html
Utilities/javascript/FindScaffoldORFS.html
Utilities/javascript/Scaffold.html
Utilities/javascript/style.css
Utilities/krona/extractTaxonomy.pl
Utilities/krona/GetContigMagnitudesCA.pl
Utilities/krona/GetContigMagnitudesNewbler.pl
Utilities/krona/ImportBLAST.pl
Utilities/krona/ImportMETAREP.pl
Utilities/krona/ImportMGRAST.pl
Utilities/krona/ImportPHMMER.pl
Utilities/krona/ImportPhyloSift.pl
Utilities/krona/ImportPhymmBL.pl
Utilities/krona/ImportText.pl
Utilities/krona/ImportXML.pl
Utilities/krona/indexGIs.pl
Utilities/krona/Krona.pm
Utilities/krona/updateTaxonomy.sh
Utilities/perl/amphora_install.pl
Utilities/perl/combine_fasta.pl
Utilities/perl/combine_fasta_qual.pl
Utilities/perl/combine_fastq.pl
Utilities/perl/compute_mates.pl
Utilities/perl/fasta2apg.pl
Utilities/perl/get_coverage.pl
Utilities/perl/get_singles.pl
Utilities/perl/ImportFCP.pl
Utilities/perl/ImportMetaPhyler.pl
Utilities/perl/ImportPhyloSift.pl
Utilities/perl/ImportPhymmBL.pl
Utilities/perl/make12.pl
Utilities/perl/makemaster.pl
Utilities/perl/metaphyler_contigs.pl
Utilities/perl/phylosift_install.pl
Utilities/perl/prinseq-lite.pl
Utilities/perl/prinseq.pl
Utilities/perl/run_FragGeneScan.pl
Utilities/perl/runblast.pl
Utilities/perl/runsoap.pl
Utilities/perl/scoreCombined.pl
Utilities/perl/scoreReads.pl
Utilities/perl/shuffleSequences_fasta.pl
Utilities/perl/shuffleSequences_fastq.pl
Utilities/perl/split_fasta.pl
Utilities/perl/split_fastq.pl
Utilities/perl/statistics.pl
Utilities/perl/update_blastdb.pl
Utilities/python/AddModel.py
Utilities/python/annotate_contigs.py
Utilities/python/BLASTN.py
Utilities/python/BuildBlastDB.py
Utilities/python/create_mapping.py
Utilities/python/create_plots.py
Utilities/python/create_report.py
Utilities/python/create_summary.py
Utilities/python/create_tigr_contig_file.py
Utilities/python/Epsilon-NB.py
Utilities/python/examples.py
Utilities/python/extract_mates_from_fasta.py
Utilities/python/extract_mates_from_fastq.py
Utilities/python/extract_soap_contigs.py
Utilities/python/fasta2fastq.py
Utilities/python/fastq_to_fasta_and_qual.py
Utilities/python/fixcontig.py
Utilities/python/get_classify_stats.py
Utilities/python/get_setuptools.py
Utilities/python/getContigRepeats.py
Utilities/python/goBambus2.py
Utilities/python/helper.py
Utilities/python/LCA+Epsilon-NB.py
Utilities/python/LCA.py
Utilities/python/markup.py
Utilities/python/NB-BL.py
Utilities/python/NB_install.py
Utilities/python/pie.py
Utilities/python/pygooglechart.py
Utilities/python/run_reports.py
Utilities/python/settings.py
Utilities/python/sff_extract_0_2_8.py
Utilities/python/sort_contigs.py
Utilities/python/splitfasta.py
Utilities/python/TaxonomicSummary.py
Utilities/python/taxonomy.txt
Utilities/python/test_server.py
Utilities/R/Coverage.R
Utilities/ruffus/__init__.py
Utilities/ruffus/adjacent_pairs_iterate.py
Utilities/ruffus/cmdline.py
Utilities/ruffus/file_name_parameters.py
Utilities/ruffus/graph.py
Utilities/ruffus/print_dependencies.py
Utilities/ruffus/proxy_logger.py
Utilities/ruffus/re_glob.py
Utilities/ruffus/ruffus_exceptions.py
Utilities/ruffus/ruffus_utility.py
Utilities/ruffus/ruffus_version.py
Utilities/ruffus/svn-commit.tmp
Utilities/ruffus/task.py
Utilities/ruffus/test/complicated_example.py
Utilities/ruffus/test/create_test_script_from_dependency_tree.py
Utilities/ruffus/test/draw_specified_dependency_tree.py
Utilities/ruffus/test/play_with_colours.py
Utilities/ruffus/test/qrsh_workaround.py
Utilities/ruffus/test/run_all_unit_tests.cmd
Utilities/ruffus/test/simpler.py
Utilities/ruffus/test/simpler_at_runtime.py
Utilities/ruffus/test/simpler_with_shared_logging.py
Utilities/ruffus/test/test_branching_dependencies.py
Utilities/ruffus/test/test_collate.py
Utilities/ruffus/test/test_empty_files_decorator.py
Utilities/ruffus/test/test_exceptions.py
Utilities/ruffus/test/test_file_name_parameters.py
Utilities/ruffus/test/test_files_decorator.py
Utilities/ruffus/test/test_files_post_merge.py
Utilities/ruffus/test/test_filesre_combine.py
Utilities/ruffus/test/test_filesre_split_and_combine.py
Utilities/ruffus/test/test_follows_mkdir.py
Utilities/ruffus/test/test_inputs_with_multiple_args_raising_exception.py
Utilities/ruffus/test/test_N_x_M_and_collate.py
Utilities/ruffus/test/test_pausing.py
Utilities/ruffus/test/test_ruffus_utility.py
Utilities/ruffus/test/test_script.py_template
Utilities/ruffus/test/test_split_and_combine.py
Utilities/ruffus/test/test_split_regex_and_collate.py
Utilities/ruffus/test/test_task_file_dependencies.py
Utilities/ruffus/test/test_task_misc.py
Utilities/ruffus/test/test_transform_add_inputs.py
Utilities/ruffus/test/test_transform_inputs.py
Utilities/ruffus/test/test_transform_with_no_re_matches.py
Utilities/ruffus/test/test_tutorial7.py
Utilities/ruffus/test/test_unicode_filenames.py
Utilities/ruffus/test/auto_generated_pipeline_examples/parallel.py
Utilities/ruffus/test/auto_generated_pipeline_examples/simple.py
Utilities/ruffus/test/auto_generated_pipeline_examples/simpler.py
Utilities/ruffus/test/data_for_complicated_example/all_genes_in_each_species/fly.genes.fa
Utilities/ruffus/test/data_for_complicated_example/all_genes_in_each_species/octopus.genes.fa
Utilities/ruffus/test/data_for_complicated_example/all_genes_in_each_species/spider.genes.fa
Utilities/ruffus/test/data_for_complicated_example/all_genes_in_each_species/worm.genes.fa
Utilities/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets1.genes.fa
Utilities/ruffus/test/data_for_complicated_example/unknown_genes/gene_sets2.genes.fa
Utilities/ruffus/test/dependency_data/dag.dependency
Utilities/ruffus/test/dependency_data/non_dag.dependency
Utilities/ruffus/test/dependency_data/simple.dag
Utilities/ruffus/test/dependency_data/simpler.dag