Salmon - Classify Reads

Find closest homologue sequence for each sequenced fragment

Location

• Filepath: <SnakeLines_dir>/rules/paired_end/classification/transcripts/salmon.snake
• Rule name: salmon__classify_reads

Input(s):

• r1: Left side of sequenced fragments in gzipped fastq format
• r2: Right side of sequenced fragments in gzipped fastq format
• index: One of index files generated by Salmon

Output(s):

• counts: TSV file with estimated taxonomic counts for each transcript

Salmon - Create Reference Index

Transform transcriptomic sequences into Salmon index for faster classification

Location

• Filepath: <SnakeLines_dir>/rules/paired_end/classification/transcripts/salmon.snake
• Rule name: salmon__create_reference_index

Input(s):

• fasta: Genomic reference sequences of transcripts

Output(s):

• index: One of index files generated by Salmon

Salmon - Prepare For Krona

Convert Salmon classification files into standardised format suitable for generation of Krona reports

Location

• Filepath: <SnakeLines_dir>/rules/paired_end/classification/transcripts/salmon.snake
• Rule name: salmon__prepare_for_krona

Input(s):

• counts: Read counts from Salmon

Output(s):

• krona: Tabular format suitable for Krona report generation