SQT(1)

🌸 SQT — SeQuencing Tools for biological DNA/RNA high-throughput data 🧬✨

okay bestie, sit down, hydrate, because this is the toolkit you've been waiting for 💖

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📛 NAME

sqt — SeQuencing Tools for biological DNA/RNA high-throughput data. yes that's the whole name, it's giving "I'm a binary and I contain multitudes" 💅

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🎀 DESCRIPTION

so like, here's the vibe check 👑

usage: sqt [-h] [--version]

       {align, bam2fastq, fastxmod, qgramfreq, chars, fastagrep,
       readcov, randomseq, samsetop, bameof, readlenhisto, cutvect} ...

SeQuencing Tools — command-line tools for working with sequencing data. that's the mission statement, no cap 🌈

basically sqt is your main character hub and it's got a whole little squad of subcommands underneath it. pick one, run it, slay. ✨

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🫶 positional arguments:

the squad, in order, exactly as they come:

• {align, bam2fastq, fastxmod, qgramfreq, chars, fastagrep, readcov, randomseq, samsetop, bameof, readlenhisto, cutvect} — that's the full roster, and every single one of them is described right below ⬇️
• align — compare two strings. just two. head to head. may the best string win 💅
• bam2fastq — pull every read out of a BAM file that maps to a certain location, but try hard. like, really commit. the effort is the whole point 🫡
• fastxmod — modify FASTA and FASTQ files by picking subsets and modifying individual entries. glow-up but for your sequence records ✨
• qgramfreq — print q-gram (also called k-mer) frequencies in a FASTA or FASTQ file. same thing, two names, iykyk 🔥
• chars — print the number of characters in a string. short king behavior 👑
• fastagrep — search for a IUPAC string in the sequences of a FASTA file. grep, but make it biology 🧬
• readcov — print a report for individual reads in a SAM/BAM file. receipts for every read 📋
• randomseq — generate random sequences in FASTA format. chaos, but formatted correctly 🎲
• samsetop — perform set operation on two SAM/BAM files. set theory found alive and well in bioinformatics 🌸
• bameof — check whether the EOF marker is present in BAM files. is it there or is it not, we must know 👀
• readlenhisto — print and optionally plot a read length histogram of one or more FASTA or FASTQ. data visualization era 📊
• cutvect — remove vector sequence. bye-bye vector, we don't know her ✂️

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💖 optional arguments:

the classic duo, both iconic, both essential:

• -h, --help — show this help message and exit. your bestie when you're lost 🥺
• --version — show program's version number and exit. for when you need to know which era of sqt you're living in 💫

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✍️ AUTHOR

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, king behavior, we appreciate you 🫶💜

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ok so real talk, quick recap bestie: sqt = the hub, twelve subcommands = the squad, -h and --version = your two flags, and that's literally it. no hidden lore. go forth and sequence 🌈✨

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sqt 0.8.0 🌸 January 2019 🎀 and that's the whole manual page, mwah 💋