blast

virpipe blast --image IMAGE --prefix PREFIX [--outdir OUTDIR] \
                     [--resume] --fasta FASTA \
                     --blast-db [BLAST_DB] [--min-evalue 1.0e-5] \
                     [--min-blast-aln-len 100 \
                     --taxonomizr-db [TAXONOMIZR_DB]

The task blast is for running BLAST with input .fasta file. BLAST results get associated with taxonomies by taxonomizr and exported as tables with useful features in HTML format. Two applications, blastn and megablast, are utilized.

Used tools

BLAST, taxonomizr

Options

• --blast-db: (Path) Database for BLAST. Please note that it should be the directory + basename of indexes. For example, if the path of the database directory is /path/to/dir/blast_db and it contains indexes such as refseq_viral.nhr, refseq_viral.nog, and so on, /path/to/dir/blast_db/refseq_viral should be given to this option.
• --min-evalue: (String, default 1.0e-5) Threshold for E-value ranged from 0 to 1. The results whose evalue is less than this value remain. The lower threshold is set, the more certain BLAST results are left.
• --min-blast-aln-len: (Int, default 100) Threshold for alignment length.
• --taxonomizr-db: (File) Database for taxonomizr. It has .sql extension. For example, accessionTaxa.sql