Salmon - Classify Reads --------------------------- Find closest homologue sequence for each sequenced fragment **Location** - *Filepath:* /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:* /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:* /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