Custom - Summarize Taxonomic Counts Into Tsv Table

Take taxonomic counts and proportions from several samples and merge them together into a single table. Also calculate number of reads per sample for each taxonomic unit.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/taxonomic_counts/count_table/custom.snake
  • Rule name: custom__summarize_taxonomic_counts_into_tsv_table

Input(s):

  • krns: Taxonomy files for each analysed sample in standardised format suitable for Krona graph generation

Output(s):

  • summary_xlsx: Aggregated counts for each discovered taxonomy in Excel format
  • summary_tsv: Aggregated counts for each discovered taxonomy in tabular format
  • subtax_xlsx: Aggregated counts for each discovered taxonomy and its subtaxes in Excel format
  • subtax_tsv: Aggregated counts for each discovered taxonomy and its subtaxes in tabular format
  • subtax_xlsx: Normalised (counts for sample sum to 1) aggregated counts for each discovered taxonomy and its subtaxes in Excel format
  • subtax_tsv: Normalised (counts for sample sum to 1) aggregated counts for each discovered taxonomy and its subtaxes in tabular format

Custom - Extract Taxonomic Level From Taxonomic Table

Extract read counts for organisms at selected taxonomic level, such as genus, species.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/taxonomic_counts/count_table/custom.snake
  • Rule name: custom__extract_taxonomic_level_from_taxonomic_table

Input(s):

  • subtax_tsv: Aggregated counts for each discovered taxonomy and its subtaxes in tabular format

Output(s):

  • tax_level_abs: Aggregated counts for single taxonomic level, e.g. species, order
  • tax_level_rel: Normalised (counts for a sample sum to 1) aggregated counts for single taxonomic level, e.g. species, order