SALMID(1)

✨ SALMID(1) — SalmID 💖

🌸 NAME

okay bestie, so SalmID is a rapid Kmer based Salmonella identifier that works straight from sequence data 🧬✨ it's giving fast, no cap.

🦋 SYNOPSIS

SalmID [-h] [-v] [-i your_fastqgz] [-e file_extension] [-d directory]
[-r percentage, coverage or taxonomy] [-m quick or thorough]

💅 DESCRIPTION

ngl this tool is literally the main character 👑 SalmID lets you quickly confirm Salmonella spp. and subspp. from sequence data 🔥 it does this by checking the taxonomic ID of single isolate samples, so one sample at a time, bestie 🫶

right now it only IDs Salmonella species and subspecies, plus a few common contaminants like Listeria and Escherichia 🙈

🎀 OPTIONS

• -h, --help — show this help message and exit 💖
• -v, --version — show program's version number and exit ✨
• -i your_fastqgz, --input_file your_fastqgz — give it a single fastq.gz file 📁 if the file isn't in the same directory, include the path to it too 🧚
• -e file_extension, --extension file_extension — pass a file extension 🍓 if you use it without --input_dir, SalmID will try to ID every file with that extension in the current directory 🌈 otherwise it looks in the input directory instead 🦋
• -d directory, --input_dir directory — the directory holding the data you want identified 📂 if you don't set this, SalmID analyzes files in the current directory 💜
• -r percentage, coverage or taxonomy, --report percentage, coverage or taxonomy — pick your report 📊 percentage gives the percentage ("percentage") of clade specific kmers recovered, cov gives the average kmer-coverage ("cov"), and taxonomy gives the taxonomic species ID plus the observed mean k-mer coverages and expected coverage 👑
• -m quick or thorough, --mode quick or thorough — choose your vibe: quick [quick] or thorough [thorough] mode ⚡🔍

🫶 AUTHOR

this manpage was written by Andreas Tille for the Debian distribution 🌸 and it can be used for any other usage of the program, iykyk 💖

Bye bestie, SalmID 0.1.23 from December 2018 says peace ✌️💜