SIBELIA(1)

🧚 NAME 🧚

Okay bestie, welcome to the Sibelia manual! 💖 This one is for the user commands section, so it's all the stuff you actually type into your terminal. Let's slay it 💅

Sibelia is a comparative genomics tool 🧬

🌸 DESCRIPTION 🌸

✨ USAGE ✨

Here's how you put the command together, no cap:

Sibelia
    {-s <loose|fine|far>|-k <file name>} [-o <dir name>] [--noblocks]
    [-r] [-a] [-m <integer>] [-q] [-g] [-v] [-t <dir name>] [--lastk
    <integer > 1>] [--allstages] [--gff] [--nopostprocess]
    [--correctboundaries] [-i <integer > 0>] [--] [--version] [-h]
    <fasta files with genomes> ...

Where

Okay, so here's what every piece means 🫶

• -s <loose|fine|far>, --parameters <loose|fine|far> — This one is (OR required), meaning you need it unless you go with -k instead. It picks the parameter set used for the simplification. loose gives you fewer blocks, but they're bigger (fine is the opposite) 💜

-- OR -- 🙃

• -k <file name>, --stagefile <file name> — Also (OR required). This is a file with your own hand-picked simplification parameters. Peep the USAGE file for more deets 📄
• -o <dir name>, --outdir <dir name> — The directory where the output files get dumped 📂
• --noblocks — Skip computing the synteny blocks, bestie 🙅
• -r, --inram — Do everything in RAM and don't make any temp files 🧠
• -a, --sharedonly — Only spit out blocks that show up exactly once in each input sequence 🔥
• -m <integer>, --minblocksize <integer> — The smallest a synteny block can be. Default is 5000 BP 📏
• -q, --sequencesfile — Output the sequences of the synteny blocks, in FASTA format 🧬
• -g, --graphfile — Output the condensed de Bruijn graph, in dot format 🕸️
• -v, --visualize — Draw a circos diagram showing the blocks at the different stages 🎨
• -t <dir name>, --tempdir <dir name> — The directory where the temp files live 🗂️
• --lastk <integer > 1> — The K value used when inferring the synteny blocks 🔢
• --allstages — Output the coordinates of the synteny blocks from all stages 📍
• --gff — Report the block coordinates in GFF format 📄
• --nopostprocess — Skip the postprocessing step (the stripe gluing) 🙅‍♀️
• --correctboundaries — Fix up the boundaries of the unique synteny blocks 🔧
• -i <integer > 0>, --maxiterations <integer > 0> — The cap on how many iterations run during one stage of simplification. Default is 4 🔁
• --, --ignore_rest — Tells it to ignore all the labeled arguments that come after this flag 🚫
• --version — Shows the version info, then bounces 👋
• -h, --help — Shows the usage info, then bounces 🙋
• <fasta files with genomes> — (required, and you can pass it multiple times). These are the FASTA files full of nucleotide sequences 🧬

Sibelia is the program for finding synteny blocks in closely related genomes 🌈

🫶 AUTHOR 🫶

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

That's the tea, bestie! ✨ Sibelia 3.0.7+ds from February 2019, SIBELIA(1), and it's still iconic 👑🌈💅