akutils format_database

akutils format_database - format a database for a specific primer set

Usage (order is important!!):

akutils format_database  <input_fasta> <input_taxonomy> <input_primers> <read_length> <output_directory> <input_phylogeny>  

This script will take an input reference fasta, an associated taxonomy file already formatted for use with QIIME, and a pair of primers (degenerate OK) and produces four pairs of fasta and taxonomy files as outputs:

1. read1 (for use with read 1 only)
2. read2 (for use with read 2 only)
3. amplicon (for use with joined data)
4. composite (combines the other three outputs for maximum completeness)

Tree file:
If a phylogeny is supplied (tree file), an associated tree will be filtered for each pair of taxonomy and fasta files.

Primers file:
<input_primers> must be formatted for Primer Prospector and contain no more than two primers. Example:

515f    GTGCCAGCMGCCGCGGTAA  
806r    GGACTACHVGGGTWTCTAAT  

Notes: Primer suffixes (f and r) are essential. Primer sequences are supplied 5->3 prime. Database fasta must be correctly oriented with respect to primer direction. Input files can have only ONE "." character immediately preceeding the file extension or this workflow will fail.

Example:

akutils format_database greengenes_97repset.fasta greengenes_97tax.txt 515-806.txt 150 16S_v4_db  

The example will take representative sequences and associated taxonomy file for greengenes97 and use the primer file 515-806.txt to produce a set of database files for use with v4 amplicons generated with 515f and 806r in paired end 2x150 mode. Output will be placed in a directory called 16S_v4_db.

Citations:
Please cite Primer Prospector if you find this utility useful.

PrimerProspector: de novo design and taxonomic analysis of PCR primers (2011). William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, and Rob Knight. Bioinformatics 27(8):1159-1161.