Fast_Virome_Explorer - Estimate Virome Composition ------------------------------------------------------ Asses viral composition of sample based on read_counts of particular taxonomic units. **Location** - *Filepath:* /rules/paired_end/classification/read_based/fast_virome_explorer.snake - *Rule name:* fast_virome_explorer__estimate_virome_composition **Input(s):** - *reads_f:* fastq file with sequences from forward strand - *reads_r:* fastq file with sequences from reverse strand - *index:* kallisto index created from reference database - *ref_lens:* lenghts of particular reference genomes from database **Output(s):** - *composition:* TSV table containing information about number of reads assigned to taxonomic units (most common species) - *abundance:* TSV table containing NCBI ID of all found taxonomic units with assigned read counts and transkripts per milion Custom - Fill Na Values With Virusnames ------------------------------------------- Python script, replaces blank space in input TSV file with virus names from that row and create new changed TSV file. **Location** - *Filepath:* /rules/paired_end/classification/read_based/fast_virome_explorer.snake - *Rule name:* custom__fill_na_values_with_virusnames **Input(s):** - *composition:* TSV table containing information about number of reads assigned to taxonomic units (most common species), generated as output of previous rule **Output(s):** - *checked_composition:* new TSV table but that NA values replace with virus names from first column Custom - Convert To Tpm Metric ---------------------------------- Python script (have to be set in config => count_type: tpm), create new TSV table with metric turned into tpm (transcripts per milion). **Location** - *Filepath:* /rules/paired_end/classification/read_based/fast_virome_explorer.snake - *Rule name:* custom__convert_to_tpm_metric **Input(s):** - *checked_composition:* checked TSV table in previous rule, containing information about number of reads assigned to taxonomic units (most common species) - *abundance:* TSV table containing NCBI ID of all found taxonomic units with assigned read counts and transkripts per milion, output from rule fast_virome_explorer__estimate_virome_composition **Output(s):** - *checked_tpm_composition:* new TSV table but that count metric is changed from read count to tpm Custom - Convert To Krona ----------------------------- Create from input file new krona file. **Location** - *Filepath:* /rules/paired_end/classification/read_based/fast_virome_explorer.snake - *Rule name:* custom__convert_to_krona **Input(s):** - *composition:* containing information about number of reads assigned to taxonomic units (most common species), output file from one of the last two previous rules (according to selected count metric) **Output(s):** - *krona:* new krona file Metaxa2 - Classify Reads ---------------------------- Find closest homologue sequence for each sequenced fragment **Location** - *Filepath:* /rules/paired_end/classification/read_based/metaxa2.snake - *Rule name:* metaxa2__classify_reads **Input(s):** - *r1:* Left side of sequenced fragments in gzipped fastq format - *r2:* Right side of sequenced fragments in gzipped fastq format - *blast:* Blast index of reference sequences (generated by Metaxa2 database builder) - *cutoffs:* Auxiliary files from reference sequences (generated by Metaxa2 database builder) - *hmm:* Auxiliary file from reference sequences (generated by Metaxa2 database builder) **Output(s):** - *taxonomy:* Summary taxonomies of classified sequenced fragments Metaxa2 - Create Reference Index ------------------------------------ Transform genomic sequences into Metaxa2 index for faster classification **Location** - *Filepath:* /rules/paired_end/classification/read_based/metaxa2.snake - *Rule name:* metaxa2__create_reference_index **Input(s):** - *fasta:* Genomic reference sequences in Fasta format - *tax:* Taxonomies for each reference sequence **Output(s):** - *blast:* Blast index of reference sequences - *cutoffs:* Auxiliary files from reference sequences - *hmm:* Auxiliary file from reference sequences Metaxa2 - Summarize Classification -------------------------------------- Summarize taxonomies per individual taxonomic levels - e.g. for species, order ... **Location** - *Filepath:* /rules/paired_end/classification/read_based/metaxa2.snake - *Rule name:* metaxa2__summarize_classification **Input(s):** - *taxonomy:* Classified fragments - output of metaxa2 tool - *nomatch_template:* Auxiliary file for margin case without any classified fragment - *nomatch_tax_template:* Auxiliary file for margin case without any classified fragment **Output(s):** - *summary:* Summarized taxonomy per species level (others should be generated accordingly) Metaxa2 - Prepare For Krona ------------------------------- Convert metaxa2 classification files into standardised format suitable for generation of Krona reports **Location** - *Filepath:* /rules/paired_end/classification/read_based/metaxa2.snake - *Rule name:* metaxa2__prepare_for_krona **Input(s):** - *classification:* Summarized classification from Metaxa2 classifier **Output(s):** - *krona:* Tabular format suitable for Krona report generation Rdp - Classify Reads ------------------------ Find closest homologue sequence for each sequenced fragment **Location** - *Filepath:* /rules/paired_end/classification/read_based/rdp.snake - *Rule name:* rdp__classify_reads **Input(s):** - *reads:* Joined sequenced fragments in fasta format **Output(s):** - *readtax:* Individual taxonomy for each analysed fragment - *taxonomy:* Summary taxonomies of classified sequenced fragments Rdp - Prepare For Krona --------------------------- Convert RDP classification files into standardised format suitable for generation of Krona reports **Location** - *Filepath:* /rules/paired_end/classification/read_based/rdp.snake - *Rule name:* rdp__prepare_for_krona **Input(s):** - *classification:* Summarized classification from RDP classifier **Output(s):** - *krona:* Tabular format suitable for Krona report generation