akutils primer_file

akutils primer_file - manage your primer_file.txt for use with strip_primers command

Usage:

akutils primer_file  

Puts user into interactive script for producing a new primer_file.txt using sequences from the akutils primer database. Use akutils primer_list to see available primers. Script provides options for adding new primer sequences or removing existing ones from either the user file or the database itself.

Sequence orientation:
If removing primers from 3' end of reads, use reverse/complemented sequences. In the akutils primer database these have the "rc" suffix. This is the most common usage.

For directional primer removal (3' or 5' modes), primer name used to generate first sequencing read should be first in the file, primer name used to generate second sequencing read should be second in the file. In the example below, the primer file contents are appropriate for 16S V4 sequencing when the first read is generated with 515F and the second read is generated with 806R.

Example primer file contents:

515Frc	GTGCCAGCMGCCGCGGTAA  
806Rrc	GGACTACHVGGGTWTCTAAT  

List of available primers:
To view the list of available primer sequences in the akutils database, you can call the primer list with:

akutils primer_list  

-- primer sequence names with "rc" suffix indicate reverse-complemented  
    sequences, appropriate for most 3' primer/adapter removal tasks.  
-- use "q" to exit screen.