index info

[macmanes]

Current:

Usage: paladin index [options] <reference.fasta> [annotation.gff]

Algorithm options:

       -f       Enable indexing all frames in nucleotide references
       -r<#>    Reference type:
                   0: Reference contains nucleotide sequences (requires annotation)
                   1: Reference contains nucleotide sequences (coding only)
                   2: Reference contains protein sequences
                   3: Development tests

Should add a little more info:

Reference contains nucleotide sequences (requires corresponding .gff annotation file)
Reference contains nucleotide sequences (coding only, e.g., a curated transcriptome)
Reference contains protein sequences (from UniProt or another source)

Also a sample command

Sample Command:

        paladin index -r2 uniprot_sprot.fasta

[ToniWestbrook]

Done