akutils strip_primers

akutils strip_primers - remove primer sequences from your amplicon reads

Usage (order is important!):

akutils strip_primers <mode> <read1> <read2> <index1> <index2>  

    Requires a primer file to be present (primer_file.txt).  
        -- only processes up to the first two primers in the file.  
    Must supply at least one valid fastq file with .fq or .fastq extension.  
    <mode> -- Two digits denoting trimming mode and count of supplied indexes.  
        First digit:	0, 1, or 2 -- the number of index files supplied.  
        Second digit:	3, 5, or B -- end to trim primers from.  

Output:
Resulting files will be output to a subdirectory called strip_primers_out and appended with the primers and filtering mode.

Examples:

akutils strip_primers 13 read1.fq read2.fq index1.fq  

    13 denotes a single index file and 3' trimming (most common)  

akutils strip_primers 25 read1.fq read2.fq index1.fq index2.fq  

    25 denotes two index files and anchored 5' trimming  

akutils strip_primers 1B read1.fq read2.fq index1.fq  

    1B denotes a single index file and primer trimming at both ends  

Primer file:
Requires primer_file.txt to function. If not present, will call the primer_file function in akutils to produce one. Can modify this file further (or create a new one) with the the primer_file command:

akutils primer_file  

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  

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.

5' trimming should use forward sequences. 5' trimming is needed when the start of your sequence contains a PCR primer. This happens when "universal" sequencing primers are used.

If your sequence could occur on either end, use the "B" option. Will search the same sequence on both ends (does not reverse complement).

Configurable settings (akutils config file):

Cutadapt_errors	-- Amount of primer mismatch allowed (decimal)  

This script trims primers from input fastqs. In some cases this can result in fastq lines which contain no sequence (empty record). This script will reconcile such empty records against any supplied index files in order to keep data in phase.

Requires the following dependencies to run:

1. cutadapt
2. QIIME 1.9.1