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1. oligo_file_maker oligo_file_maker Public

   This script reads information about qPCR primers and probes from a csv file and creates the various oligonucleotide files required by the qPCR Screener pipeline (i.e. oligonucleotide definition csv…

   Python 1 1

2. findOligosInSequence findOligosInSequence Public

   Searches nucleotide fasta sequences for exact matches to oligonucleotides (i.e. primers, probes) and their reverse complements. If exact matches to all oligos are not found, outputs the (i) sequenc…

   Python

3. find_amplicon_in_sequence find_amplicon_in_sequence Public

   Searches nucleotide fasta sequences for an exact match to a PCR amplicon and outputs full-length un-matching sequences to fasta.

   Python

4. extract_amplicon_from_primersearch_output extract_amplicon_from_primersearch_output Public

   Extracts PCR amplicons from full-length nucleotide fasta sequences, using Emboss primersearch output.

   Python

5. amplicon_sequevars_to_dict amplicon_sequevars_to_dict Public

   Sorts nucleotide fasta sequences into a dictionary that maps unique sequences to lists of sequence records sharing the sequence. Excludes sequences matching those from in an optional fasta file of …

   Python

6. extract_oligo_hyb_regions_from_amplicon_sequevars extract_oligo_hyb_regions_from_amplicon_sequevars Public

   Extracts theoretical oligonucleotide hybridization sites from PCR amplicon sequences in a fasta file and outputs concatenated hybridization sites to fasta.

   Python