LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
q2_assembly/__init__.py
q2_assembly/_action_params.py
q2_assembly/_utils.py
q2_assembly/_version.py
q2_assembly/citations.bib
q2_assembly/plugin_setup.py
q2_assembly.egg-info/PKG-INFO
q2_assembly.egg-info/SOURCES.txt
q2_assembly.egg-info/dependency_links.txt
q2_assembly.egg-info/entry_points.txt
q2_assembly.egg-info/not-zip-safe
q2_assembly.egg-info/top_level.txt
q2_assembly/assets/quast/index.html
q2_assembly/assets/quast/q2_icarus.html
q2_assembly/assets/quast/q2_krona_charts.html
q2_assembly/bowtie2/__init__.py
q2_assembly/bowtie2/indexing.py
q2_assembly/bowtie2/mapping.py
q2_assembly/bowtie2/utils.py
q2_assembly/bowtie2/tests/__init__.py
q2_assembly/bowtie2/tests/test_indexing.py
q2_assembly/bowtie2/tests/test_mapping.py
q2_assembly/bowtie2/tests/test_utils.py
q2_assembly/bowtie2/tests/data/manifest-paired.csv
q2_assembly/bowtie2/tests/data/manifest-single.csv
q2_assembly/bowtie2/tests/data/manifest-wrong-samples.csv
q2_assembly/bowtie2/tests/data/contigs/sample1_contigs.fa
q2_assembly/bowtie2/tests/data/contigs/sample2_contigs.fa
q2_assembly/bowtie2/tests/data/empty_contigs/empty_contigs.fa
q2_assembly/bowtie2/tests/data/empty_contigs/sample1_contigs.fa
q2_assembly/bowtie2/tests/data/empty_contigs/second_empty_contigs.fa
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.1.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.2.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.3.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.4.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.rev.1.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample1/index.rev.2.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.1.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.2.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.3.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.4.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.rev.1.bt2
q2_assembly/bowtie2/tests/data/indices/from_contigs/sample2/index.rev.2.bt2
q2_assembly/bowtie2/tests/data/mags/sample1/mag1.fa
q2_assembly/bowtie2/tests/data/mags/sample1/mag2.fa
q2_assembly/bowtie2/tests/data/mags/sample2/mag1.fa
q2_assembly/bowtie2/tests/data/mags/sample2/mag2.fa
q2_assembly/bowtie2/tests/data/maps/from_contigs/sample1.bam
q2_assembly/bowtie2/tests/data/maps/from_contigs/sample2.bam
q2_assembly/bowtie2/tests/data/reads/paired-end/MANIFEST
q2_assembly/bowtie2/tests/data/reads/paired-end/reads1_R1.fastq.gz
q2_assembly/bowtie2/tests/data/reads/paired-end/reads1_R2.fastq.gz
q2_assembly/bowtie2/tests/data/reads/paired-end/reads2_R1.fastq.gz
q2_assembly/bowtie2/tests/data/reads/paired-end/reads2_R2.fastq.gz
q2_assembly/bowtie2/tests/data/reads/single-end/MANIFEST
q2_assembly/bowtie2/tests/data/reads/single-end/reads1_R1.fastq.gz
q2_assembly/bowtie2/tests/data/reads/single-end/reads2_R1.fastq.gz
q2_assembly/helpers/__init__.py
q2_assembly/helpers/helpers.py
q2_assembly/iss/__init__.py
q2_assembly/iss/iss.py
q2_assembly/iss/tests/__init__.py
q2_assembly/iss/tests/test_iss.py
q2_assembly/iss/tests/data/abundances/biom_table.tsv
q2_assembly/iss/tests/data/abundances/samp1_abundance.txt
q2_assembly/iss/tests/data/abundances/samp2_abundance.txt
q2_assembly/iss/tests/data/genomes/genomes1.fasta
q2_assembly/iss/tests/data/genomes/genomes2.fasta
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q2_assembly/iss/tests/data/reads/sample1_00_L001_R2_001.fastq.gz
q2_assembly/iss/tests/data/reads/sample2_00_L001_R1_001.fastq.gz
q2_assembly/iss/tests/data/reads/sample2_00_L001_R2_001.fastq.gz
q2_assembly/megahit/__init__.py
q2_assembly/megahit/megahit.py
q2_assembly/megahit/tests/__init__.py
q2_assembly/megahit/tests/test_megahit.py
q2_assembly/quast/__init__.py
q2_assembly/quast/quast.py
q2_assembly/quast/tests/__init__.py
q2_assembly/quast/tests/test_quast.py
q2_assembly/spades/__init__.py
q2_assembly/spades/spades.py
q2_assembly/spades/tests/__init__.py
q2_assembly/spades/tests/test_spades.py
q2_assembly/tests/__init__.py
q2_assembly/tests/test_utils.py
q2_assembly/tests/data/sample_contigs.fa
q2_assembly/tests/data/contigs/sample1_contigs.fa
q2_assembly/tests/data/contigs/sample2_contigs.fa
q2_assembly/tests/data/formatted-reads/paired-end/MANIFEST
q2_assembly/tests/data/formatted-reads/paired-end/metadata.yml
q2_assembly/tests/data/formatted-reads/paired-end/sample1_f_L001_R1_001.fastq.gz
q2_assembly/tests/data/formatted-reads/paired-end/sample1_r_L001_R2_001.fastq.gz
q2_assembly/tests/data/formatted-reads/paired-end/sample2_f_L001_R1_001.fastq.gz
q2_assembly/tests/data/formatted-reads/paired-end/sample2_r_L001_R2_001.fastq.gz
q2_assembly/tests/data/formatted-reads/single-end/MANIFEST
q2_assembly/tests/data/formatted-reads/single-end/metadata.yml
q2_assembly/tests/data/formatted-reads/single-end/sample1_f_L001_R1_001.fastq.gz
q2_assembly/tests/data/formatted-reads/single-end/sample2_f_L001_R1_001.fastq.gz
q2_assembly/tests/data/html-files/sample-report-div-removed.html
q2_assembly/tests/data/html-files/sample-report-links-updated.html
q2_assembly/tests/data/html-files/sample-report.html
q2_assembly/tests/data/html-files/fake-reports/report.html
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q2_assembly/tests/data/html-files/fake-reports/expected/report.html
q2_assembly/tests/data/html-files/fake-reports/icarus_viewers/contig_size_viewer.html
q2_assembly/tests/data/reads/paired-end/MANIFEST
q2_assembly/tests/data/reads/paired-end/reads1_R1.fastq.gz
q2_assembly/tests/data/reads/paired-end/reads1_R2.fastq.gz
q2_assembly/tests/data/reads/paired-end/reads2_R1.fastq.gz
q2_assembly/tests/data/reads/paired-end/reads2_R2.fastq.gz
q2_assembly/tests/data/reads/single-end/MANIFEST
q2_assembly/tests/data/reads/single-end/reads1_R1.fastq.gz
q2_assembly/tests/data/reads/single-end/reads2_R1.fastq.gz
q2_assembly/tests/data/reads/single-sample/paired-end/MANIFEST
q2_assembly/tests/data/reads/single-sample/paired-end/reads1_R1.fastq.gz
q2_assembly/tests/data/reads/single-sample/paired-end/reads1_R2.fastq.gz
q2_assembly/tests/data/reads/single-sample/single-end/MANIFEST
q2_assembly/tests/data/reads/single-sample/single-end/reads1_R1.fastq.gz
q2_assembly/tests/data/reads/small-single-end/concat_samples.fastq
q2_assembly/tests/data/reads/small-single-end/sample1_00_L001_R1_001.fastq
q2_assembly/tests/data/reads/small-single-end/sample2_00_L001_R1_001.fastq
q2_assembly/tests/data/references/ref1.fasta
q2_assembly/tests/data/references/ref2.fasta
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