├── ._wb ├── launcher │ ├── gigmap_docker │ │ ├── config.json │ │ └── run.sh │ └── gigmap_slurm │ │ ├── config.json │ │ └── run.sh └── tool │ ├── align_genomes │ ├── config.json │ └── run.sh │ ├── align_pangenome │ ├── config.json │ └── run.sh │ ├── align_reads │ ├── config.json │ └── run.sh │ ├── ani │ ├── config.json │ └── run.sh │ ├── build_pangenome │ ├── config.json │ └── run.sh │ ├── collect │ ├── config.json │ └── run.sh │ ├── deduplicate_genes │ ├── config.json │ └── run.sh │ ├── download_genes │ ├── config.json │ └── run.sh │ ├── download_genomes │ ├── config.json │ └── run.sh │ ├── map_genes │ ├── config.json │ └── run.sh │ ├── pdist │ ├── config.json │ └── run.sh │ ├── render │ ├── config.json │ └── run.sh │ ├── search_sketches │ ├── config.json │ └── run.sh │ ├── sketch_genomes │ ├── config.json │ └── run.sh │ └── test_reads │ ├── config.json │ └── run.sh ├── .gitignore ├── Dockerfile ├── README.md ├── __init__.py ├── align_genomes.nf ├── align_pangenome.nf ├── align_reads.nf ├── ani.nf ├── app ├── __init__.py ├── cartesian_tree.py ├── figure_builder.py ├── gig-map ├── gig-map-cli ├── gig_map_elements.py ├── helpers.py └── plotly_subplots.py ├── bin ├── aggregate_results.py ├── bin_genes.py ├── bin_summary.py ├── cluster_genomes.py ├── collect_metagenomes.py ├── deduplicate_fasta_names.py ├── deduplicate_gene_names.sh ├── extract_genes.py ├── extract_markers.py ├── filter_alignments.py ├── format_geneshot_annotations.py ├── gather_alignments.py ├── generate_gene_map.py ├── merge_cluster_membership.py ├── order_genes.py ├── parse_preview_json.py ├── plot_bins.py ├── plot_metagenomes.py ├── plot_regress.py ├── reorganize_fastas.py ├── reorganize_markers.py ├── select_markers.py ├── serialize.py ├── subset_alignments_by_genes.py └── wide_bin_abundance.py ├── bin_genes.nf ├── bin_metagenomes.nf ├── collect.nf ├── contrast_metagenomes.nf ├── deduplicate.nf ├── download_genes.nf ├── download_genomes.nf ├── example_files ├── config_aws │ └── nextflow.config ├── config_docker │ └── nextflow.config ├── config_singularity │ └── nextflow.config ├── run_align │ ├── align.params.json │ └── align.sh ├── run_deduplicate │ ├── deduplicate.params.json │ └── deduplicate.sh ├── run_download │ ├── download.params.json │ └── download.sh ├── run_render │ ├── render.params.json │ └── render.sh └── screenshots │ └── Screen Shot 2021-12-14 at 3.48.19 PM.png ├── helpers.gvy ├── map_genes.nf ├── modules ├── aggregate.nf ├── align_genomes.nf ├── align_markers.nf ├── align_reads.nf ├── ani.nf ├── bin_genes.nf ├── bin_metagenomes.nf ├── build_trees.nf ├── collect.nf ├── contrast_metagenomes.nf ├── deduplicate.nf ├── download_genes.nf ├── download_genomes.nf ├── filter_genomes.nf ├── find_reads.nf ├── import_geneshot.nf ├── import_metagenome.nf ├── processes │ ├── aggregate.nf │ ├── align_genes.nf │ ├── align_genomes.nf │ ├── align_reads.nf │ ├── ani.nf │ ├── assign_metadata.nf │ ├── bin_genes.nf │ ├── bin_metagenomes.nf │ ├── deduplicate.nf │ ├── download.nf │ ├── general.nf │ ├── import_geneshot.nf │ └── map_genes.nf ├── render.nf ├── sketch_genomes.nf └── test_reads.nf ├── nextflow.config ├── output └── output.dnd ├── pdist.nf ├── render.nf ├── requirements.txt ├── search_sketches.nf ├── setup.cfg ├── setup.py ├── sketch_genomes.nf ├── templates ├── aggregate_distances.py ├── aggregate_results.sh ├── align_reads.sh ├── annotate_centroids.py ├── calc_distmat.py ├── cdhit.sh ├── centroids.annot.csv.gz ├── centroids_length.py ├── clean_genomes.sh ├── collect_pdist.py ├── concat_csv.py ├── concat_readcounts.py ├── concatenate_alignments.py ├── concatenate_annotations.py ├── diamond_logs.py ├── famli.sh ├── famli_logs.py ├── fetchFTP.py ├── filter_aln.py ├── filter_genes.py ├── filter_genomes_ids.py ├── filter_msas.py ├── find_orfs.sh ├── genome_annotations.csv ├── getDatasets.sh ├── get_gene_annot.py ├── group_sketches.sh ├── join.py ├── join_pdist.py ├── map_genes_blast.sh ├── map_genes_diamond.sh ├── map_genes_filter.py ├── map_genes_join.py ├── map_genes_shard.py ├── merge_bins.py ├── metadata.csv ├── parse_genome_csv.py ├── parse_genome_tsv.py ├── parse_manifest.py ├── raxml.sh ├── reformat.py ├── regress.Rscript ├── render_params.json ├── search.sh ├── shard_genes.py └── sketch.sh ├── test.sh ├── test_data ├── Escherichia_virus_T4.csv ├── GCA_000005845.2_ASM584v2_protein.annotations.csv ├── GCA_000005845.2_ASM584v2_protein.dmnd ├── GCA_000005845.2_ASM584v2_protein.faa.gz ├── GCA_002599665.1_ASM259966v1_protein.dmnd ├── GCA_002599665.1_ASM259966v1_protein.faa.gz ├── NCBI_Escherichia_coli_genomes.csv ├── NCBI_Escherichia_coli_genomes.test_subset.annotations.csv ├── NCBI_Escherichia_coli_genomes.test_subset.csv ├── cpn60.fasta.gz ├── fastq │ ├── SRR19177897_1.fastq.gz │ ├── SRR19177897_2.fastq.gz │ ├── SRR19178189_1.fastq.gz │ └── SRR19178189_2.fastq.gz ├── launch_wb.sh ├── output.csv.gz ├── output.dists.tsv.gz ├── output.rdb ├── read_manifest.csv ├── run_tests.sh └── tests.bats └── test_reads.nf 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