LICENSE.md
MANIFEST.in
README.md
setup.py
amptk/Guilds.py
amptk/OTU_cluster.py
amptk/OTU_cluster_ref.py
amptk/__init__.py
amptk/__version__.py
amptk/amptklib.py
amptk/assign_taxonomy.py
amptk/barcode_rarify.py
amptk/check_version.R
amptk/collapse_taxonomy.py
amptk/csv2heatmap.py
amptk/dada2.py
amptk/dada2_pacbio.py
amptk/dada2_pipeline_nofilt.R
amptk/drop.py
amptk/extract_region.py
amptk/fastq2sra.py
amptk/filter.py
amptk/get_barcode_counts.py
amptk/heatmap.py
amptk/info.py
amptk/install.py
amptk/keep_samples.py
amptk/lulu.py
amptk/merge_metadata.py
amptk/newsummary.py
amptk/parse_adonis.py
amptk/phyloseq_nmds.R
amptk/phyloseq_nmds_indicator.R
amptk/process_illumina2.py
amptk/process_illumina_folder.py
amptk/process_illumina_raw.py
amptk/process_ion.py
amptk/process_ont.py
amptk/process_pacbio.py
amptk/pybam.py
amptk/remove_samples.py
amptk/runLULU.R
amptk/stackedBarGraph.py
amptk/stats.py
amptk/summarize_taxonomy.py
amptk/unoise2.py
amptk/unoise3.py
amptk.egg-info/PKG-INFO
amptk.egg-info/SOURCES.txt
amptk.egg-info/dependency_links.txt
amptk.egg-info/requires.txt
amptk.egg-info/top_level.txt
amptk/DB/.DS_Store
amptk/DB/amptk_mock1.fa
amptk/DB/amptk_mock2.fa
amptk/DB/amptk_mock3.fa
amptk/DB/amptk_synmock.fa
amptk/DB/ioncode_barcodes.fa
amptk/DB/ionxpress_barcodes.fa
docs/.gitignore
docs/Makefile
docs/amptk.pdf
docs/clustering.rst
docs/commands.rst
docs/conf.py
docs/downstream.rst
docs/file-formats.rst
docs/filtering.rst
docs/index.rst
docs/make.bat
docs/overview.rst
docs/pre-processing.rst
docs/quick-start.rst
docs/stats-page.png
docs/stats.pdf
docs/summarize-percent.pdf
docs/summarize.pdf
docs/taxonomy.rst
scripts/.DS_Store
scripts/amptk
scripts/amptk_synthetic_mock.py
scripts/bold2utax.py
test_data/.DS_Store
test_data/Run1_R1.fastq
test_data/Run1_R2.fastq
test_data/barcode_1.fa
test_data/barcode_2.fa
test_data/dada2.amptk-dada2.log
test_data/dada2.cleaned_input.fq
test_data/illumina2.amptk-demux.log
test_data/illumina2.barcodes_used.fa
test_data/illumina2.demux.fq.gz
test_data/illumina2.mapping_file.txt
test_data/illumina2.revbarcodes_used.fa
test_data/illumina2_map.amptk-demux.log
test_data/illumina2_map.demux.fq.gz
test_data/illumina2_map.mapping_file.txt
test_data/ion.amptk-demux.log
test_data/ion.barcodes_used.fa
test_data/ion.demux.fq.gz
test_data/ion.mapping_file.txt
test_data/ion.test.fastq
test_data/ion_2mm.amptk-demux.log
test_data/ion_2mm.barcodes_used.fa
test_data/ion_2mm.demux.fq.gz
test_data/ion_2mm.mapping_file.txt
test_data/ion_map.amptk-demux.log
test_data/ion_map.demux.fq.gz
test_data/ion_map.mapping_file.txt
test_data/miseq-dada2.amptk-dada2.log
test_data/miseq-dada2.cleaned_input.fq
test_data/miseq-dada2.dada2.Rscript.log
test_data/miseq-dada2.original.fa
test_data/miseq-dada2.qual-filtered.fq
test_data/miseq.amptk-demux.log
test_data/miseq.demux.fq.gz
test_data/miseq.filenames.txt
test_data/miseq.mapping_file.txt
test_data/miseq2.amptk-demux.log
test_data/miseq2.demux.fq.gz
test_data/miseq2.filenames.txt
test_data/miseq2.mapping_file.txt
test_data/miseq3.amptk-demux.log
test_data/miseq3.demux.fq.gz
test_data/miseq3.filenames.txt
test_data/miseq3.mapping_file.txt
test_data/miseq_map.amptk-demux.log
test_data/miseq_map.demux.fq.gz
test_data/miseq_map.filenames.txt
test_data/miseq_map.mapping_file.txt
test_data/run1_mapping_file.txt
test_data/run_tests.sh
test_data/test.demux.fq.gz
test_data/test_R1.fastq
test_data/test_R2.fastq