├── .coveragerc ├── .github └── workflows │ └── ci.yaml ├── .gitignore ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── bit ├── __init__.py ├── cli │ ├── __init__.py │ ├── assemble.py │ ├── calc_gc_per_seq.py │ ├── calc_gc_sliding_window.py │ ├── calc_variation_in_msa.py │ ├── check_for_fastq_dup_headers.py │ ├── common.py │ ├── cov_analyzer.py │ ├── ez_screen.py │ ├── filter_fasta_by_length.py │ ├── gen_kraken2_tax_plots.py │ ├── gen_reads.py │ ├── get_cov_stats.py │ ├── kraken2_to_taxon_summaries.py │ ├── summarize_assembly.py │ └── summarize_column.py ├── modules │ ├── __init__.py │ ├── assemble.py │ ├── cov_analyzer.py │ ├── ez_screen.py │ ├── gen_kraken2_tax_plots.py │ ├── gen_reads.py │ ├── general.py │ ├── get_cov_stats.py │ ├── input_parsing.py │ ├── kraken2_to_taxon_summaries.py │ └── seqs.py ├── scripts │ ├── bit-GL-combine-KO-and-tax-tables │ ├── bit-GL-combine-contig-tax-tables │ ├── bit-assemble │ ├── bit-calc │ ├── bit-calc-gc-per-sequence │ ├── bit-calc-gc-sliding-window │ ├── bit-calc-variation-in-msa │ ├── bit-check-for-fastq-dup-headers │ ├── bit-colnames │ ├── bit-combine-bracken-and-add-lineage │ ├── bit-combine-go-summaries │ ├── bit-combine-kraken2-taxon-summaries │ ├── bit-count-bases │ ├── bit-count-bases-per-seq │ ├── bit-cov-analyzer │ ├── bit-data-locations │ ├── bit-dedupe-fasta-headers │ ├── bit-dl-ncbi-assemblies │ ├── bit-extract-seqs-by-coords │ ├── bit-ez-screen │ ├── bit-fasta-to-bed │ ├── bit-fasta-to-genbank │ ├── bit-figshare-upload │ ├── bit-filter-KOFamScan-results │ ├── bit-filter-fasta-by-length │ ├── bit-filter-seqs-by-length │ ├── bit-filter-table │ ├── bit-gen-iToL-binary-dataset │ ├── bit-gen-iToL-colorstrip │ ├── bit-gen-iToL-map │ ├── bit-gen-iToL-text-dataset │ ├── bit-gen-kraken2-tax-plots │ ├── bit-gen-reads │ ├── bit-genbank-locus-clean-slate │ ├── bit-genbank-to-AA-seqs │ ├── bit-genbank-to-cds-table │ ├── bit-genbank-to-fasta │ ├── bit-get-accessions-from-GTDB │ ├── bit-get-cov-stats │ ├── bit-get-go-term-info │ ├── bit-get-lineage-from-taxids │ ├── bit-get-test-data │ ├── bit-get-workflow │ ├── bit-gff-to-anvio │ ├── bit-kraken2-to-taxon-summaries │ ├── bit-lineage-to-tsv │ ├── bit-mutate-seqs │ ├── bit-normalize-table │ ├── bit-parse-fasta-by-headers │ ├── bit-parse-fastq-by-headers │ ├── bit-prot-acc-to-taxid │ ├── bit-remove-wraps │ ├── bit-rename-fasta-headers │ ├── bit-reorder-fasta │ ├── bit-slim-down-go-terms │ ├── bit-split-multifasta │ ├── bit-summarize-assembly │ ├── bit-summarize-column │ ├── bit-summarize-go-annotations │ ├── bit-update-go-dbs │ ├── bit-update-ncbi-taxonomy │ ├── bit-version │ ├── helper-bit-check-or-setup-GTDB-files.py │ ├── helper-bit-combine-bracken.py │ ├── helper-bit-dl-ncbi-assemblies-parallel.sh │ ├── helper-bit-get-ncbi-assembly-tables │ ├── helper-bit-get-ncbi-tax-data │ ├── helper-bit-parse-assembly-summary-file.py │ ├── helper-bit-setup-GO-dbs │ └── helper-bit-update-tax-table-for-seqscreen-go-tax-summary.sh ├── smk │ ├── __init__.py │ ├── assemble.smk │ ├── envs │ │ ├── assemble-osx-64.yaml │ │ └── assemble.yaml │ └── ez-screen-reads.smk └── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ ├── ez-screen-R1.fastq.gz │ ├── ez-screen-R2.fastq.gz │ ├── ez-screen-assembly.fasta │ ├── ez-screen-targets.fasta │ ├── ez-screen.bam │ ├── ez-screen.bam.bai │ ├── kraken-example-out.tsv │ ├── kraken-example.report │ ├── mock-R1.fastq.gz │ └── mock-R2.fastq.gz │ ├── test_assemble.py │ ├── test_cov_analyzer.py │ ├── test_ez_screen.py │ ├── test_gen_kraken2_tax_plots.py │ ├── test_gen_reads.py │ ├── test_general.py │ ├── test_get_cov_stats.py │ ├── test_input_parsing.py │ ├── test_kraken2_to_taxon_summaries.py │ ├── test_seqs.py │ ├── test_summarize_assembly.py │ ├── test_summarize_column.py │ └── utils.py ├── conda-recipe ├── build.sh ├── meta.yaml └── post-link.sh ├── dev-link.sh ├── images ├── bit-cov-analyzer.pdf ├── bit-cov-analyzer.png ├── bit-metagenomics-overview.afdesign ├── bit-metagenomics-overview.pdf └── bit-metagenomics-overview.png ├── pyproject.toml ├── pytest.ini ├── setup.py ├── update-conda-package.sh └── workflows ├── genome-summarize-wf ├── README.md ├── Snakefile ├── config.yaml ├── envs │ ├── bit.yaml │ ├── cat.yaml │ ├── checkm2.yaml │ ├── eukcc.yaml │ └── gtdb-tk.yaml └── scripts │ ├── combine-euk-outputs.py │ ├── combine-outputs.py │ └── slurm-status.py ├── metagenomics-wf ├── CHANGELOG.md ├── README.md ├── Snakefile ├── config.yaml ├── config │ └── multiqc.config ├── envs │ ├── bit.yaml │ ├── cat.yaml │ ├── checkm2.yaml │ ├── gtdb-tk.yaml │ ├── keggdecoder.yaml │ ├── kofamscan.yaml │ ├── mapping.yaml │ ├── megahit.yaml │ ├── metabat.yaml │ ├── prodigal.yaml │ └── qc.yaml └── scripts │ ├── combine-benchmarks.sh │ ├── download-gtdbtk-refs.sh │ ├── format-contig-tax-classifications.sh │ ├── format-gene-tax-classifications.sh │ ├── generate-assembly-based-overview-table.sh │ ├── parse-MAG-annots.py │ ├── slurm-status.py │ └── swap-MAG-IDs.py 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