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cds_extractor

Script for extracting Coding DNA Sequence (CDS) values from a GB file.

contigcounter

Parses BLAST result files and tabulates the top hits for each query and prints out a report.

fizzz

(File Size Subdirectory Sorter - Fizzz/Fisss) - Small (and rather project-specific) utility that takes a list of files or files in a directory and moves them into a user-specified number of folders such that the total size of each folder is roughly the same.

forward-email

:envelope: :fast_forward: ForwardEmail is a free, encrypted, and open-source email forwarding service for custom domains. Visit our website to get started.

mlstar

A script that matches and returns an ST type number for a given base reference sequence, MLST fragment files (all fasta formatted), and ST type table file.

phrecon

Phrecon (PHylo RECONstructor) -- This script reconstructs the base sequence using an SNP loci and substituting its bases in at the given locations in the provided reference base sequence.

prephix

Prephix (Pre-Phrecon Input fiXer) -- This is a script that takes in a list of input files and generates one SNP loci output file (containing multiple strains), one reference base file, and a file containing the excluded indel entries.

pterrs

ENA Project ERS -> ERR lookup/linker

pyregexfilerenamer

Python 3 TKInter app for doing mass file renaming using regexes.

snp_swapper

This script reconstructs the base sequence using a base reference sequence in FASTA format, and a SNP loci file and indel file produced by prephix. It then does substituting, inserting, or deleting of the base sequence bases at the given locations in the provided reference base sequence. It writes out a separate regenerated base sequence for each strain in the SNP input file.

snpeffectplus

snpfx

This is a 2018 modified version for a Nature Genetics publication. It is basically a modified version of what is in the SNPEffectPlus repo, separted out for citation purposes.

twstak

TradeWars 2002 Simple Telnet Auto Keyer (macro app)