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atlas_output_files.yaml
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atlas_output_files.yaml
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# a list of all atlas output files copatible with atlas V 2.13
v2:
readcounts: "stats/read_counts.tsv"
genomes:
taxonomy: "genomes/taxonomy/gtdb_taxonomy.tsv"
tree_bacteria: "genomes/tree/gtdbtk.bac120.nwk"
quality: "genomes/checkm/completeness.tsv"
counts : "genomes/counts/raw_counts_genomes.tsv"
coverage: "genomes/counts/median_coverage_genomes.tsv"
keggmodules: "genomes/annotations/dram/kegg_modules.tsv"
v2.13:
readcounts: "stats/read_counts.tsv"
genomes:
taxonomy: "genomes/taxonomy/gtdb_taxonomy.tsv"
tree_bacteria: "genomes/tree/gtdbtk.bac120.nwk"
quality: "genomes/genome_quality.tsv"
counts : "genomes/counts/raw_counts_genomes.tsv"
coverage: "genomes/counts/median_coverage_genomes.tsv"
keggmodules: "genomes/annotations/dram/kegg_modules.tsv"
genecatalog:
coverage: Genecatalog/counts/median_coverage.parquet
counts: Genecatalog/counts/Nmapped_reads.parquet
geneinfo: Genecatalog/clustering/orf_info.parquet
v2.16:
stats: "stats"
reports: "reports"
readcounts: "stats/read_counts.tsv"
genomes:
taxonomy: "genomes/taxonomy/gtdb_taxonomy.tsv"
tree_bacteria: "genomes/tree/gtdbtk.bac120.nwk"
quality: "genomes/genome_quality.tsv"
counts : "genomes/counts/counts_genomes.parquet"
coverage: "genomes/counts/median_coverage_genomes.parquet"
keggmodules: "genomes/annotations/dram/kegg_modules.tsv"
dram: "genomes/annotations/dram/annotations.tsv"
dram_report: "genomes/annotations/dram/product.html"
dram_xlsx: "genomes/annotations/dram/metabolism_summary.xlsx"
gene2genomes: "genomes/annotations/gene2genome.parquet"
bin2genome: genomes/clustering/allbins2genome.tsv
vamb: # final binner might be other than vamb
similarities: Binning/vamb/genome_similarities.parquet
bin_info: Binning/vamb/filtered_bin_info.tsv
report: reports/bin_report_vamb.html
dastool: # final binner might be other than vamb
similarities: Binning/DASTool/genome_similarities.parquet
bin_info: Binning/DASTool/filtered_bin_info.tsv
report: reports/bin_report_DASTool.html
semibin: # final binner might be other than vamb
similarities: Binning/SemiBin/genome_similarities.parquet
bin_info: Binning/SemiBin/filtered_bin_info.tsv
report: reports/bin_report_SemiBin.html
genecatalog:
coverage_stats: Genecatalog/counts/gene_coverage_stats.parquet
coverage: Genecatalog/counts/median_coverage.h5
counts: Genecatalog/counts/Nmapped_reads.h5
sample_stats: Genecatalog/counts/sample_coverage_stats.tsv
geneinfo: Genecatalog/clustering/orf_info.parquet
eggnog: Genecatalog/annotations/eggNOG.parquet
kegg: Genecatalog/annotations/dram/kegg.parquet
cazy: Genecatalog/annotations/dram/cazy.parquet
pfam: Genecatalog/annotations/dram/pfam.parquet
v2.17:
config: "config.yaml"
sampletable: "samples.tsv"
stats: "stats"
reports: "reports"
readcounts: "stats/read_counts.tsv"
genomes:
taxonomy: "genomes/taxonomy/gtdb_taxonomy.tsv"
tree_bacteria: "genomes/tree/gtdbtk.bac120.nwk"
quality: "genomes/genome_quality.tsv"
counts : "genomes/counts/counts_genomes.parquet"
coverage: "genomes/counts/median_coverage_genomes.parquet"
keggmodules: "genomes/annotations/dram/kegg_modules.tsv"
dram: "genomes/annotations/dram/annotations.tsv"
dram_report: "genomes/annotations/dram/distil/product.html"
dram_xlsx: "genomes/annotations/dram/distil/metabolism_summary.xlsx"
gene2genomes: "genomes/annotations/gene2genome.parquet"
bin2genome: genomes/clustering/allbins2genome.tsv
vamb: # final binner might be other than vamb
similarities: Binning/vamb/genome_similarities.parquet
bin_info: Binning/vamb/bin_info.tsv
bin2species: Binning/vamb/bins2species.tsv
report: reports/bin_report_vamb.html
dastool: # final binner might be other than vamb
similarities: Binning/DASTool/genome_similarities.parquet
bin_info: Binning/DASTool/bin_info.tsv
bin2species: Binning/DASTool/bins2species.tsv
report: reports/bin_report_DASTool.html
semibin: # final binner might be other than vamb
similarities: Binning/SemiBin/genome_similarities.parquet
bin_info: Binning/SemiBin/bin_info.tsv
bin2species: Binning/SemiBin/bins2species.tsv
report: reports/bin_report_SemiBin.html
genecatalog:
coverage_stats: Genecatalog/counts/gene_coverage_stats.parquet
coverage: Genecatalog/counts/median_coverage.h5
counts: Genecatalog/counts/Nmapped_reads.h5
sample_stats: Genecatalog/counts/sample_coverage_stats.tsv
geneinfo: Genecatalog/clustering/orf_info.parquet
eggnog: Genecatalog/annotations/eggNOG.parquet
kegg: Genecatalog/annotations/dram/kegg.parquet
cazy: Genecatalog/annotations/dram/cazy.parquet
pfam: Genecatalog/annotations/dram/pfam.parquet
strains: "strains/comparison/output"
strains_pdf: "strains/comparison/figures"