– Generates predicted amplicons and reads from primers


Using hits files (generated with, this module will look at an individual primer or a specified primer pair to generate amplicons and reads. By default, the weighted score is used to determine if a particular primer will amplify, but other results (3’ mismatches, overall mismatches) can be used to determine if a primer will amplify. Every fasta file used to generate the hits file must be passed to this module (multiple fastas should be separated by a colon). If a single hits file is specified, the amplicon will be the entire sequence following the 3’ end of the primer.

Usage: [options]

Input Arguments:



-i, --primer_hits
Target primer hits files. Separate multiple files with a colon.
-f, --fasta_fps
Fasta filepaths. Must match the fasta files used in the analyze_primers module. Multiple fasta files can be passed, separated with a colon. Order not important.


-o, --output_dir
Specify output directory for amplicons and reads. [default: .]
-s, --score_type
Value to use from primer hits file to determine a given primer’s amplification success. Valid choices are weighted_score, overall_mismatches, tp_mismatches. Gibbs energy scores not currently implemented [default: weighted_score]
-t, --score_threshold
If primer has score at or below this parameter, the primer amplification is considered to be successful [default: 1.0]
-m, --min_seq_len
Sets minimum sequence length of amplicon to be included in the output amplicon file [default: 100]
-d, --read_direction
Direction of reads generated. Can be forward (f), reverse (r), or paired end (p). [default: r]
-R, --read_len
Length of reads to generate. Should be set according to sequencing technology/reagents used. [default: 250]


An amplicon file (in fasta format) will be written for the forward and reverse primer pair, with a name based upon the name of the primers (taken from hits file name, e.g. 27f_338r_amplicons.fasta). The reads file will be generated in the same manner, with an “_reads” instead of “_amplicons”.

Standard Example usage (examine pair of primer hits files): [options] {-f fasta_filepath -i primer_hits_filepath1:primer_hits_filepath2 [required] }

Use total mismatches instead of weighted score to determine if a given primer will amplify: -f fasta_filepath -i primer_hits_filepath1:primer_hits_filepath2 -s total_mismatches

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