Bio::T...Tradis(3pm)

💖 Bio::T...Tradis — the Bio::Tradis::RunTradis page, but make it make sense 💖

okay bestie, so this is Bio::T...Tradis(3pm) from the User Contributed Perl Documentation, and honestly? it's giving pipeline energy. let's get into it 🧚

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✨ NAME ✨

Bio::Tradis::RunTradis — does every single step you need for a tradis analysis. the whole glow-up, start to finish. no cap. 💅

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🌸 VERSION 🌸

version 1.4.5 — she's been updated, she's thriving.

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🦋 SYNOPSIS 🦋

so basically: you hand her a fastq file that already has tags attached, she filters the tags that match what you asked for, she removes those tags, maps everything to a reference (.fa), and then she pops out insertion site plots for Artemis (or whatever other genome browser you're feeling that day), mapped BAM files for each lane, AND a statistical summary of the whole analysis. she does it all, periodt. 👑

use Bio::Tradis::RunTradis;

my $pipeline = Bio::Tradis::RunTradis->new(
                                     fastqfile => 'abc',
                                     reference => 'abc',
                                     tag => 'abc',
                                     tagdirection => '5'|'3'
);
$pipeline->run_tradis();

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🎀 PARAMETERS 🎀

💜 Required

these ones? non-negotiable. you have to give her these, fr fr.

• fastqfile — the file containing a list of fastqs (gzipped or raw, she's not picky) that you want to run the complete analysis on. and when we say complete, we mean complete — this covers all the steps, including all the intermediary format conversion and sorting, starting right from filtering. the whole journey. 🚀
• reference — path to / name of your reference genome in fasta format (.fa). she needs to know where home is.

🌈 Optional

these are the little extras. the accessories to the outfit. adorable, but not mandatory. ✨

• mismatch — how many mismatches to allow when filtering/removing the tag. Default = 0. zero. strict. she's not playing. 💀
• tagdirection — the direction of the tag, either 5' or 3'. Default = 3.
• mapping_score — the cutoff value for mapping score when she's creating those insertion site plots. Default = 30.
• tag — the TraDIS tag to filter and then remove. yeah. exactly that. 🏷️

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🫶 METHODS 🫶

• run_tradis — runs the complete analysis with the parameters you gave her. that's it, that's the method, she ate. 🍽️

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👑 AUTHOR 👑

Carla Cummins <path-help@sanger.ac.uk> — the icon, the legend, the moment.

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💖 COPYRIGHT AND LICENSE 💖

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007

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and that's the whole page bestie!! mwah 💋

this little masterpiece lives in perl v5.30.0, dated 2020-01-11, and it's filed under Bio::T...Tradis(3pm) — iykyk 🌟 go run your tradis analysis, you absolute main character 🦋💅