SUBLONG(1)

💅 SUBLONG 💅

okay bestie, gather round, because this one is a whole toolkit and she is serving next-gen sequencing realness. yes, that's the actual manual name: sublong. it lives in section 1 of the manual (User Commands, iykyk), and she is here to process your next-gen sequencing data. no cap. 🧬✨

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🌸 NAME 🌸

sublong — a toolkit for processing next-gen sequencing data 🦋

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🎀 DESCRIPTION 🎀

okay so first things first, the page itself is like "please specify the input, output files and the index." that's it. that's the vibe check. the program is NOT going to guess for you, you have to actually tell her what she's working with. 💀

this is Sublong v2.0.4, and here's how you actually run her:

./sublong [options] -i <index_name> -r <input> -o <output>

👑 Mandatory arguments

these are not optional, bestie. she literally cannot function without them. main character requirements. 🔥

• -i <string> — the base name of the index. important: the index has to be built as a full index and it has only one block. that's the rule, periodt. don't come at her with a partial index, she will simply not.
• -r <string> — the name of an input read file. the formats she'll accept are gzipped FASTQ and FASTQ, and she figures out which one it is automatically, so you don't have to announce it like it's a gender reveal. 🙈
• -o <string> — the name of your output file, and it has to be in BAM format. that's the assignment. 💜

✨ Optional arguments: # input reads and output

this is where you get to customise, and honestly? obsessed. 🫶

• --SAMoutput — save the mapping results in SAM format instead. you get options, you get range, you get flexibility. ⭐

🧚 # number of CPU threads

• -T <int> — how many CPU threads she gets to use. default is 1, so if you want her to actually go fast, speak up and hand her more. lowkey a glow-up waiting to happen. 🔥

🌈 # others

• -v — output the version of the program. short, sweet, iconic.
• -X — turn on the RNA-seq mode. yes, a whole different mode. she contains multitudes. 🦋

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📖 and if you want the detailed description of all these arguments, the page says to refer to the Users Manual. she's not gonna spell every last thing out here, that's what the manual is for. go read it, bestie, i believe in you. 💖

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🍓 AUTHOR 🍓

this manpage was written by Alexandre Mestiashvili for the Debian distribution, and it can be used for any other usage of the program. giving credit where credit is due, as we always do. 👑

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and that's the whole page, bestie!! this is sublong version 2.0.3 (yes, the footer says 2.0.3 while the description says v2.0.4, i don't make the rules, i just report them 💀), dated March 2023, from the SUBLONG(1) manual. now go specify your input, output, and index and slay. 💅✨