Each script comes with its own help description
Determine the number of nearby SNPs using a SNP table. Useful for designing primers.
Run with arguments from command line
Input: Table with sorted SNP positions. First two columns must be 1)Chromosome 2)Position
Output: For each SNP, the number of nearby SNPs in a specified window, and the location of the closest SNP
-i input: Input table that has 1)CHR 2)POS
-o ouput: Output table
-r range: Integer range of bases around SNP to look for other snps
-s skip: Number of lines to skip for headings in input file. Default is that header is present(1)
Mask a reference assembly by a list of snp positions (CHR,POS). Replace the allele at a given position with a user-specified allele
Useful for primer design or masking known problematics regions of a assembly
NOTE: makes replacements within FASTA file - it is recommended to backup the FASTA file first.
-i input: Input FASTA file
-p positions file: Table with [CHR POS] to mask
-a allele mask: Letter to mask bases with
Pull sequences from a FASTA file around user-specificed SNP positions.
Useful for primer design.
-i input: Input FASTA file
-o output file: Output table with sequences
-p positions file: Table with [CHR POS] to pull sequences around
-r sequence range: Integer; number of bases around SNP to grab
-f output format: Output in FASTA format or CSV (two-column)
A script to analyze selected primers and design probe sequences.
Requires a table of [CHR_POS, PRODUCT_SEQUENCE, F_PRIMER, R_PRIMER] for each locus
Use to design probes from amplicons and check primers
-i input: Input CSV with: Col1: CHR_POS; Col2: Product sequence (5'-3'); Col3: Fprimer; Col4: Rprimer
-o ouput table: Table with stats and warnings on primers
-r probe range: Integer for desired sequence length around probe