Fasta_Summary - Blast¶
Convert blast results into standardised unified format for fasta summary generation
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/summary/fasta_summary.snake
- Rule name: fasta_summary__blast
Input(s):
- blast: Blast classification with taxonomy
Output(s):
- tsv: Classification in unified format
Fasta_Summary - Coverage¶
Extract mapping coverage and store it into standardised unified format for fasta summary generation
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/summary/fasta_summary.snake
- Rule name: fasta_summary__coverage
Input(s):
- qualimap: Quality report statistics generated by Qualimap
Output(s):
- tsv: Mapping coverage in standardised unified format for fasta summary generation
Fasta_Summary - Mapped Reads¶
Get number of mapped reads to each reference sequence and convert into standardised unified format for fasta summary generation
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/summary/fasta_summary.snake
- Rule name: fasta_summary__mapped_reads
Input(s):
- bam: Mapped reads in bam format
- bai: Index for bam file with mapped reads
Output(s):
- tsv: Mapped reads per reference sequence in standardised unified format for fasta summary generation
Fasta_Summary - Copy Contigs¶
Separate sequences into individual fasta files and calculate basic statistics for each sequence. Also store statistics into standardised unified format for fasta summary generation.
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/summary/fasta_summary.snake
- Rule name: fasta_summary__copy_contigs
Input(s):
- fasta: Genomic sequences in fasta format
Output(s):
- fasta: Copy of fasta file, stored in the directory accessible from summary HTML report
- seqinfo: Statistics of genomic sequences in standardised unified format for fasta summary generation
Fasta_Summary - Summarize Annotations¶
Generate summary HTML report with several aggregated attribute sources from various tools.
Location
- Filepath: <SnakeLines_dir>/rules/paired_end/classification/report/summary/fasta_summary.snake
- Rule name: fasta_summary__summarize_annotations
Input(s):
- template: HTML template with basic report outline
- fasta: Analysed sequences in fasta format
- attrs_seqinfo: Basic statistics of genomic sequences - length, GC content, complexity…
- attrs_coverage: Mapping coverage of sequences
- attrs_mapped_reads: Mapped reads per genomic sequence
- attrs_virfinder: Probabilities of viral origin for genomic sequences - calculated by the Virfinder tool
Undocumented rules¶
WARNING: found 1 undocumented rules:
- rule fasta_summary__virfinder is UNDOCUMENTED