LICENSE
MANIFEST.in
readme.md
setup.cfg
setup.py
biobakery_workflows/__init__.py
biobakery_workflows/biobakery_workflows.py
biobakery_workflows/biobakery_workflows_databases.py
biobakery_workflows/biobakery_workflows_scripts.py
biobakery_workflows/config.py
biobakery_workflows/files.py
biobakery_workflows/utilities.py
biobakery_workflows/visualizations.py
biobakery_workflows.egg-info/PKG-INFO
biobakery_workflows.egg-info/SOURCES.txt
biobakery_workflows.egg-info/dependency_links.txt
biobakery_workflows.egg-info/entry_points.txt
biobakery_workflows.egg-info/not-zip-safe
biobakery_workflows.egg-info/requires.txt
biobakery_workflows.egg-info/top_level.txt
biobakery_workflows/Rscripts/alpha_diversity.R
biobakery_workflows/Rscripts/assign_taxonomy.R
biobakery_workflows/Rscripts/beta_diversity.R
biobakery_workflows/Rscripts/const_seq_table.R
biobakery_workflows/Rscripts/dada2_version.R
biobakery_workflows/Rscripts/filter_and_trim.R
biobakery_workflows/Rscripts/identify_primers.R
biobakery_workflows/Rscripts/learn_error_rates.R
biobakery_workflows/Rscripts/mantel_test.R
biobakery_workflows/Rscripts/merge_paired_ends.R
biobakery_workflows/Rscripts/permanova_hmp2.R
biobakery_workflows/Rscripts/phylogeny.R
biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R
biobakery_workflows/Rscripts/strainphlan_ordination_vis.R
biobakery_workflows/data/__init__.py
biobakery_workflows/data/strainphlan_species_gcf.tsv
biobakery_workflows/data/wmgx_methods.txt
biobakery_workflows/document_templates/16S.pmd
biobakery_workflows/document_templates/functional_dna.pmd
biobakery_workflows/document_templates/picard.pmd
biobakery_workflows/document_templates/quality_control_dada2.pmd
biobakery_workflows/document_templates/quality_control_paired_dna.pmd
biobakery_workflows/document_templates/quality_control_single_dna.pmd
biobakery_workflows/document_templates/quality_control_usearch.pmd
biobakery_workflows/document_templates/read_count_dada2.pmd
biobakery_workflows/document_templates/read_count_usearch.pmd
biobakery_workflows/document_templates/stats.pmd
biobakery_workflows/document_templates/stats_halla.pmd
biobakery_workflows/document_templates/stats_maaslin.pmd
biobakery_workflows/document_templates/stats_maaslin_stratified.pmd
biobakery_workflows/document_templates/stats_mantel_plots.pmd
biobakery_workflows/document_templates/stats_permanova.pmd
biobakery_workflows/document_templates/taxonomy.pmd
biobakery_workflows/document_templates/universal_vis.pmd
biobakery_workflows/document_templates/workflow_info.pmd
biobakery_workflows/scripts/anadama2_add_files_to_database.py
biobakery_workflows/scripts/annotate_genome.py
biobakery_workflows/scripts/burst_workflow.py
biobakery_workflows/scripts/check_fastq_format.py
biobakery_workflows/scripts/check_for_reverse_reads.py
biobakery_workflows/scripts/compute_species_of_interest.py
biobakery_workflows/scripts/count_features.py
biobakery_workflows/scripts/create_fasta_per_taxonomy_from_alignments.py
biobakery_workflows/scripts/create_feature_table.py
biobakery_workflows/scripts/create_image_tile.py
biobakery_workflows/scripts/create_otu_tables_from_alignments.py
biobakery_workflows/scripts/create_subsampled_demos.py
biobakery_workflows/scripts/demultiplex_split_index.py
biobakery_workflows/scripts/extract_orphan_reads.py
biobakery_workflows/scripts/generate_dual_barcode.py
biobakery_workflows/scripts/get_counts_from_humann_logs.py
biobakery_workflows/scripts/join_taxonomic_profiles.py
biobakery_workflows/scripts/merge_and_rename_fastq.py
biobakery_workflows/scripts/merge_fastq.py
biobakery_workflows/scripts/pull_out_reads_by_species_metaphlan2_results.py
biobakery_workflows/scripts/remove_if_exists.py
biobakery_workflows/scripts/remove_primers.py
biobakery_workflows/scripts/rename_data_products.py
biobakery_workflows/scripts/rename_fastq_files.py
biobakery_workflows/scripts/rename_files_to_sample_ids.py
biobakery_workflows/scripts/reverse_compliment_barcodes.py
biobakery_workflows/scripts/rna_dna_norm.py
biobakery_workflows/scripts/subset_file_by_sample_id.py
biobakery_workflows/scripts/trim_taxonomy.py
biobakery_workflows/tasks/__init__.py
biobakery_workflows/tasks/dadatwo.py
biobakery_workflows/tasks/general.py
biobakery_workflows/tasks/shotgun.py
biobakery_workflows/tasks/sixteen_s.py
biobakery_workflows/workflows/16s.py
biobakery_workflows/workflows/isolate_assembly.py
biobakery_workflows/workflows/stats.py
biobakery_workflows/workflows/vis.py
biobakery_workflows/workflows/wmgx.py
biobakery_workflows/workflows/wmgx_wmtx.py
examples/tutorial/input/HD32R1_subsample.fastq.gz
examples/tutorial/input/HD42R4_subsample.fastq.gz
examples/tutorial/input/HD48R4_subsample.fastq.gz
examples/tutorial/input/LD96R2_subsample.fastq.gz
examples/tutorial/input/LV16R4_subsample.fastq.gz
examples/tutorial/input/LV20R4_subsample.fastq.gz
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2
examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2
examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2
examples/wmgx/interleaved/demo_interleaved.fastq.gz
examples/wmgx/kneaddata_db/demo_db.1.bt2
examples/wmgx/kneaddata_db/demo_db.2.bt2
examples/wmgx/kneaddata_db/demo_db.3.bt2
examples/wmgx/kneaddata_db/demo_db.4.bt2
examples/wmgx/kneaddata_db/demo_db.rev.1.bt2
examples/wmgx/kneaddata_db/demo_db.rev.2.bt2
examples/wmgx/paired/demo1.R1.fastq.gz
examples/wmgx/paired/demo1.R2.fastq.gz
examples/wmgx/paired/demo2.R1.fastq.gz
examples/wmgx/paired/demo2.R2.fastq.gz
examples/wmgx/single/demo1.fastq.gz
examples/wmgx/single/demo2.fastq.gz
images/1618113365-16s_workflow_with_fasttree_merge_truncate_filter.jpg
images/2782656604-isolate_workflow.jpg
images/4005903235-DADA2Workflow_75percent.jpg
images/4071512812-wms_wtx_workflow.jpg
images/tutoral_workflow_info.png
images/tutorial_alpha_diversity.png
images/tutorial_halla_heatmap.png
images/tutorial_halla_heatmap_metadata.png
images/tutorial_humann_stratified_barplot.png
images/tutorial_maaslin_heatmap.png
images/tutorial_mantel_test.png
images/tutorial_pathway_heatmap.png
images/tutorial_pcoa.png
images/tutorial_permanova.png
images/tutorial_qc_barplot.png
images/tutorial_table_of_contents.png
images/tutorial_taxa_barplot.png
images/wms_workflow.png
tests/__init__.py
tests/test_utilities.py