Blast - Find Homologues --------------------------- Find homologues for input sequences stored in fasta file in query reference database. **Location** - *Filepath:* /rules/paired_end/classification/contig_based/blast.snake - *Rule name:* blast__find_homologues **Input(s):** - *blast_db:* Blast index of reference sequences, made by makeblastdb command - *fasta:* Genomic sequences to be classified **Output(s):** - *tsv:* Homologues for input sequences in tabular format **Param(s):** - *nohead:* Auxiliary file for immediate results - *header:* Auxiliary file for immediate results - *max_target_seqs:* Maximal number of homologue sequences to be reported for each query sequence - *blast_binary:* Blast tool to use - this differ in types of input files (nucleotide/protein) - *blast_database:* Prefix name of the input blast database files Blast - Annotate With Taxonomy ---------------------------------- Append additional column to the blast tabular output with the taxonomy of homology sequence **Location** - *Filepath:* /rules/paired_end/classification/contig_based/blast.snake - *Rule name:* blast__annotate_with_taxonomy **Input(s):** - *blast:* Blast tabular output - *taxes:* Preprocessed taxonomies in .pickle **Output(s):** - *blast:* Blast tabular output with additional column with the taxonomy of homology sequence Blast - Prepare Reference Index For Nucleotide -------------------------------------------------- Creates blast indices from genomic sequences. **Location** - *Filepath:* /rules/paired_end/classification/contig_based/blast.snake - *Rule name:* blast__prepare_reference_index_for_nucleotide **Input(s):** - *fa:* Genomic nucleotide sequences in fasta format **Output(s):** - *nhr:* Part of blast index - *nin:* Part of blast index - *nsq:* Part of blast index Blast - Prepare Reference Index For Protein ----------------------------------------------- Creates blast indices from protein sequences. **Location** - *Filepath:* /rules/paired_end/classification/contig_based/blast.snake - *Rule name:* blast__prepare_reference_index_for_protein **Input(s):** - *fa:* Genomic protein sequences in fasta format **Output(s):** - *phr:* Part of blast index - *pin:* Part of blast index - *psq:* Part of blast index