├── .gitignore ├── README.md ├── TODO.md ├── assets └── pipeline_overview.pdf ├── bin ├── __init__.py ├── aggregate_allele_matrices.py ├── aggregate_mapping_stats.py ├── aggregate_snp_sites.py ├── calculate_mapping_stats.py ├── collect_reference_data.py ├── create_allele_matrix.py ├── create_coverage_depth_matrices.py ├── create_snp_alignment.py ├── determine_coding_consequences.py ├── filter_allele_matrix.py ├── filter_variants.awk ├── genbank_to_fasta.py ├── get_coverage_depth.awk ├── get_het_counts.awk ├── get_passing_isolate_replicons.awk ├── get_reads_mapped.awk ├── get_snp_indels.awk ├── get_snp_sites.awk ├── merge_gene_stat_matrix.py ├── merge_mapping_stats.py ├── split_mapped_unmapped_reads.awk ├── utility.py └── validate_merge_data.py ├── config ├── conda_dependencies.txt └── slurm_job.config ├── nextflow.config ├── reddog.nf ├── src ├── channel_helpers.nf ├── merge_workflow.nf ├── processes │ ├── alignment.nf │ ├── allele_matrix.nf │ ├── mapping_stats.nf │ ├── merge.nf │ ├── misc.nf │ └── variant_calling.nf └── utilities.nf └── tests ├── __init__.py ├── data ├── allele_matrices │ ├── contig_1_isolate_18_alleles.csv │ ├── contig_1_isolate_19_alleles.csv │ ├── contig_1_isolate_1_alleles.csv │ ├── contig_1_isolate_20_alleles.csv │ ├── contig_1_isolate_21_alleles.csv │ ├── contig_1_isolate_22_alleles.csv │ ├── contig_1_isolate_23_alleles.csv │ ├── contig_1_isolate_24_alleles.csv │ ├── contig_1_isolate_25_alleles.csv │ ├── contig_1_isolate_26_alleles.csv │ ├── contig_1_isolate_27_alleles.csv │ ├── contig_1_isolate_28_alleles.csv │ ├── contig_1_isolate_29_alleles.csv │ ├── contig_1_isolate_2_alleles.csv │ ├── contig_1_isolate_30_alleles.csv │ ├── contig_1_isolate_31_alleles.csv │ ├── contig_1_isolate_32_alleles.csv │ ├── contig_1_isolate_33_alleles.csv │ ├── contig_1_isolate_34_alleles.csv │ ├── contig_1_isolate_35_alleles.csv │ ├── contig_1_isolate_36_alleles.csv │ └── contig_1_isolate_37_alleles.csv ├── expected_outputs │ ├── contig_1_alleles.csv │ ├── contig_1_alleles_cons0.95.csv │ ├── contig_1_consequences_cons0.95.tsv │ ├── contig_1_core.mfasta │ ├── contig_1_isolate_1_alleles.csv │ ├── contig_1_mapping_stats.tsv │ ├── contig_1_mapping_stats_merged.tsv │ ├── contig_2_isolate_1_alleles.csv │ ├── contig_2_mapping_stats.tsv │ ├── gene_coverage.csv │ ├── gene_coverage_merged.csv │ ├── gene_depth.csv │ ├── gene_depth_merged.csv │ ├── isolate_12_mapping_stats.tsv │ ├── isolate_1_mapping_stats.tsv │ ├── passing_isolate_replicons.tsv │ ├── reference.fasta │ └── snp_sites.tsv ├── mapping_stats │ ├── isolate_10_mapping_stats.tsv │ ├── isolate_11_mapping_stats.tsv │ ├── isolate_12_mapping_stats.tsv │ ├── isolate_13_mapping_stats.tsv │ ├── isolate_14_mapping_stats.tsv │ ├── isolate_15_mapping_stats.tsv │ ├── isolate_16_mapping_stats.tsv │ ├── isolate_17_mapping_stats.tsv │ ├── isolate_18_mapping_stats.tsv │ ├── isolate_19_mapping_stats.tsv │ ├── isolate_1_mapping_stats.tsv │ ├── isolate_20_mapping_stats.tsv │ ├── isolate_21_mapping_stats.tsv │ ├── isolate_22_mapping_stats.tsv │ ├── isolate_23_mapping_stats.tsv │ ├── isolate_24_mapping_stats.tsv │ ├── isolate_25_mapping_stats.tsv │ ├── isolate_26_mapping_stats.tsv │ ├── isolate_27_mapping_stats.tsv │ ├── isolate_28_mapping_stats.tsv │ ├── isolate_29_mapping_stats.tsv │ ├── isolate_2_mapping_stats.tsv │ ├── isolate_30_mapping_stats.tsv │ ├── isolate_31_mapping_stats.tsv │ ├── isolate_32_mapping_stats.tsv │ ├── isolate_33_mapping_stats.tsv │ ├── isolate_34_mapping_stats.tsv │ ├── isolate_35_mapping_stats.tsv │ ├── isolate_36_mapping_stats.tsv │ ├── isolate_37_mapping_stats.tsv │ ├── isolate_3_mapping_stats.tsv │ ├── isolate_4_mapping_stats.tsv │ ├── isolate_5_mapping_stats.tsv │ ├── isolate_6_mapping_stats.tsv │ ├── isolate_7_mapping_stats.tsv │ ├── isolate_8_mapping_stats.tsv │ └── isolate_9_mapping_stats.tsv ├── multiway_pileups │ ├── isolate_10_mpileup.tsv │ ├── isolate_11_mpileup.tsv │ ├── isolate_12_mpileup.tsv │ ├── isolate_13_mpileup.tsv │ ├── isolate_14_mpileup.tsv │ ├── isolate_15_mpileup.tsv │ ├── isolate_16_mpileup.tsv │ ├── isolate_17_mpileup.tsv │ ├── isolate_18_mpileup.tsv │ ├── isolate_19_mpileup.tsv │ ├── isolate_1_mpileup.tsv │ ├── isolate_20_mpileup.tsv │ ├── isolate_21_mpileup.tsv │ ├── isolate_22_mpileup.tsv │ ├── isolate_23_mpileup.tsv │ ├── isolate_24_mpileup.tsv │ ├── isolate_25_mpileup.tsv │ ├── isolate_26_mpileup.tsv │ ├── isolate_27_mpileup.tsv │ ├── isolate_28_mpileup.tsv │ ├── isolate_29_mpileup.tsv │ ├── isolate_2_mpileup.tsv │ ├── isolate_30_mpileup.tsv │ ├── isolate_31_mpileup.tsv │ ├── isolate_32_mpileup.tsv │ ├── isolate_33_mpileup.tsv │ ├── isolate_34_mpileup.tsv │ ├── isolate_35_mpileup.tsv │ ├── isolate_36_mpileup.tsv │ ├── isolate_37_mpileup.tsv │ ├── isolate_3_mpileup.tsv │ ├── isolate_4_mpileup.tsv │ ├── isolate_5_mpileup.tsv │ ├── isolate_6_mpileup.tsv │ ├── isolate_7_mpileup.tsv │ ├── isolate_8_mpileup.tsv │ └── isolate_9_mpileup.tsv ├── other │ ├── contig_1_alleles.csv │ ├── contig_1_alleles_cons0.95.csv │ ├── contig_1_mapping_stats.tsv │ ├── contig_1_mapping_stats_premerge_1.tsv │ ├── contig_1_mapping_stats_premerge_2.tsv │ ├── contig_2_mapping_stats.tsv │ ├── gene_coverage_premerge_1.csv │ ├── gene_coverage_premerge_2.csv │ ├── gene_depth_premerge_1.csv │ ├── gene_depth_premerge_2.csv │ ├── isolate_1.bam │ ├── isolate_10.sam │ ├── isolate_12.bam │ ├── isolate_12.bam.bai │ ├── isolate_12_coverage_depth.tsv │ ├── isolate_12_hets.vcf │ ├── isolate_12_q30.vcf │ ├── isolate_12_unmapped.bam │ ├── isolate_17_unmapped.bam │ ├── isolate_1_contig_1.vcf │ ├── isolate_1_coverage_depth.tsv │ ├── isolate_1_hets.vcf │ ├── isolate_1_q30.vcf │ ├── isolate_1_unmapped.bam │ ├── isolate_3_contig_1.vcf │ ├── isolate_3_hets.vcf │ ├── isolate_4_q30.vcf │ ├── passing_isolate_replicons.tsv │ ├── reference.fasta │ ├── reference.fasta.fai │ ├── reference.gbk │ ├── replicon_sites.tsv │ └── snp_sites.tsv └── snp_sites │ ├── isolate_10_sites.tsv │ ├── isolate_11_sites.tsv │ ├── isolate_12_sites.tsv │ ├── isolate_13_sites.tsv │ ├── isolate_14_sites.tsv │ ├── isolate_15_sites.tsv │ ├── isolate_16_sites.tsv │ ├── isolate_17_sites.tsv │ ├── isolate_18_sites.tsv │ ├── isolate_19_sites.tsv │ ├── isolate_1_sites.tsv │ ├── isolate_20_sites.tsv │ ├── isolate_21_sites.tsv │ ├── isolate_22_sites.tsv │ ├── isolate_23_sites.tsv │ ├── isolate_24_sites.tsv │ ├── isolate_25_sites.tsv │ ├── isolate_26_sites.tsv │ ├── isolate_27_sites.tsv │ ├── isolate_28_sites.tsv │ ├── isolate_29_sites.tsv │ ├── isolate_2_sites.tsv │ ├── isolate_30_sites.tsv │ ├── isolate_31_sites.tsv │ ├── isolate_32_sites.tsv │ ├── isolate_33_sites.tsv │ ├── isolate_34_sites.tsv │ ├── isolate_35_sites.tsv │ ├── isolate_36_sites.tsv │ ├── isolate_37_sites.tsv │ ├── isolate_3_sites.tsv │ ├── isolate_4_sites.tsv │ ├── isolate_5_sites.tsv │ ├── isolate_6_sites.tsv │ ├── isolate_7_sites.tsv │ ├── isolate_8_sites.tsv │ └── isolate_9_sites.tsv ├── simulated_data ├── CMDS ├── data │ ├── dataset_specification.tsv │ ├── reference.gbk │ └── run_data │ │ ├── bams │ │ ├── isolate_1.bam │ │ ├── isolate_10.bam │ │ ├── isolate_11.bam │ │ ├── isolate_12.bam │ │ ├── isolate_13.bam │ │ ├── isolate_14.bam │ │ ├── isolate_15.bam │ │ ├── isolate_16.bam │ │ ├── isolate_17.bam │ │ ├── isolate_18.bam │ │ ├── isolate_19.bam │ │ ├── isolate_2.bam │ │ ├── isolate_20.bam │ │ ├── isolate_21.bam │ │ ├── isolate_22.bam │ │ ├── isolate_23.bam │ │ ├── isolate_24.bam │ │ ├── isolate_25.bam │ │ ├── isolate_26.bam │ │ ├── isolate_27.bam │ │ ├── isolate_28.bam │ │ ├── isolate_29.bam │ │ ├── isolate_3.bam │ │ ├── isolate_30.bam │ │ ├── isolate_31.bam │ │ ├── isolate_32.bam │ │ ├── isolate_33.bam │ │ ├── isolate_34.bam │ │ ├── isolate_35.bam │ │ ├── isolate_36.bam │ │ ├── isolate_37.bam │ │ ├── isolate_4.bam │ │ ├── isolate_5.bam │ │ ├── isolate_6.bam │ │ ├── isolate_7.bam │ │ ├── isolate_8.bam │ │ └── isolate_9.bam │ │ ├── reference_contig_1_alleles.csv │ │ ├── reference_contig_1_alleles_cons0.95.csv │ │ ├── reference_contig_1_cons0.95.mfasta │ │ ├── reference_contig_1_cons0.95.tree │ │ ├── reference_contig_1_consequences_cons0.95.tsv │ │ ├── reference_contig_1_mapping_stats.tsv │ │ ├── reference_contig_2_alleles.csv │ │ ├── reference_contig_2_alleles_cons0.95.csv │ │ ├── reference_contig_2_cons0.95.mfasta │ │ ├── reference_contig_2_cons0.95.tree │ │ ├── reference_contig_2_consequences_cons0.95.tsv │ │ ├── reference_contig_2_mapping_stats.tsv │ │ ├── reference_gene_coverage.csv │ │ ├── reference_gene_depth.csv │ │ ├── run_info │ │ └── run_config.tsv │ │ └── vcfs │ │ ├── isolate_10_hets.vcf │ │ ├── isolate_10_q30.vcf │ │ ├── isolate_11_hets.vcf │ │ ├── isolate_11_q30.vcf │ │ ├── isolate_12_hets.vcf │ │ ├── isolate_12_q30.vcf │ │ ├── isolate_13_hets.vcf │ │ ├── isolate_13_q30.vcf │ │ ├── isolate_14_hets.vcf │ │ ├── isolate_14_q30.vcf │ │ ├── isolate_15_hets.vcf │ │ ├── isolate_15_q30.vcf │ │ ├── isolate_16_hets.vcf │ │ ├── isolate_16_q30.vcf │ │ ├── isolate_17_hets.vcf │ │ ├── isolate_17_q30.vcf │ │ ├── isolate_18_hets.vcf │ │ ├── isolate_18_q30.vcf │ │ ├── isolate_19_hets.vcf │ │ ├── isolate_19_q30.vcf │ │ ├── isolate_1_hets.vcf │ │ ├── isolate_1_q30.vcf │ │ ├── isolate_20_hets.vcf │ │ ├── isolate_20_q30.vcf │ │ ├── isolate_21_hets.vcf │ │ ├── isolate_21_q30.vcf │ │ ├── isolate_22_hets.vcf │ │ ├── isolate_22_q30.vcf │ │ ├── isolate_23_hets.vcf │ │ ├── isolate_23_q30.vcf │ │ ├── isolate_24_hets.vcf │ │ ├── isolate_24_q30.vcf │ │ ├── isolate_25_hets.vcf │ │ ├── isolate_25_q30.vcf │ │ ├── isolate_26_hets.vcf │ │ ├── isolate_26_q30.vcf │ │ ├── isolate_27_hets.vcf │ │ ├── isolate_27_q30.vcf │ │ ├── isolate_28_hets.vcf │ │ ├── isolate_28_q30.vcf │ │ ├── isolate_29_hets.vcf │ │ ├── isolate_29_q30.vcf │ │ ├── isolate_2_hets.vcf │ │ ├── isolate_2_q30.vcf │ │ ├── isolate_30_hets.vcf │ │ ├── isolate_30_q30.vcf │ │ ├── isolate_31_hets.vcf │ │ ├── isolate_31_q30.vcf │ │ ├── isolate_32_hets.vcf │ │ ├── isolate_32_q30.vcf │ │ ├── isolate_33_hets.vcf │ │ ├── isolate_33_q30.vcf │ │ ├── isolate_34_hets.vcf │ │ ├── isolate_34_q30.vcf │ │ ├── isolate_35_hets.vcf │ │ ├── isolate_35_q30.vcf │ │ ├── isolate_36_hets.vcf │ │ ├── isolate_36_q30.vcf │ │ ├── isolate_37_hets.vcf │ │ ├── isolate_37_q30.vcf │ │ ├── isolate_3_hets.vcf │ │ ├── isolate_3_q30.vcf │ │ ├── isolate_4_hets.vcf │ │ ├── isolate_4_q30.vcf │ │ ├── isolate_5_hets.vcf │ │ ├── isolate_5_q30.vcf │ │ ├── isolate_6_hets.vcf │ │ ├── isolate_6_q30.vcf │ │ ├── isolate_7_hets.vcf │ │ ├── isolate_7_q30.vcf │ │ ├── isolate_8_hets.vcf │ │ ├── isolate_8_q30.vcf │ │ ├── isolate_9_hets.vcf │ │ └── isolate_9_q30.vcf └── scripts │ ├── __init__.py │ ├── collect_genes.py │ ├── compare_data.py │ ├── generate_reference.py │ ├── simulate_reads.py │ └── utility.py ├── test_allele_matrix.py ├── test_mapping_stats.py └── test_miscellaneous.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/katholt/reddog-nf/HEAD/.gitignore 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