Bio::Tradis::Map(3pm)

🌸 Bio::Tradis::Map 💅

okay bestie, so this is the Bio::Tradis::Map page from the User Contributed Perl Documentation, and she is version 1.4.5 ✨ and honestly? she does exactly what it says on the tin.

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✨ NAME ✨

Bio::Tradis::Map — perform mapping. that's it, that's the whole vibe 🎀

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🦋 VERSION 🦋

version 1.4.5 — iconic, no notes.

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💖 SYNOPSIS 💖

so what she does is: she takes a reference genome and indexes it. then she maps the given fastq files to that ref. two-step girlie, she's organized like that 💅

use Bio::Tradis::Map;

my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
$pipeline->index_ref();
$pipeline->do_mapping();

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🌈 PARAMETERS 🌈

✨ Required ✨

these are not optional, bestie, she needs them or she's not going anywhere 😭

• fastqfile — the path to / name of the file holding the reads you wanna map to the reference 🍓
• reference — the path to / name of the reference genome, in fasta format (.fa) 👑

🎀 Optional 🎀

• refname — the name you wanna assign to the reference index files. Default = ref.index ✨
• outfile — the name you wanna assign to the mapped SAM file. Default = mapped.sam 💖

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🧚 METHODS 🧚

• index_ref — creates the index files of the reference genome. these are required for the mapping step, okay?? only skip this step if the index files already exist. the -k and -s options for referencing are calculated based on the length of the reads being mapped, as per table (the table is doing its own thing, she just says "as per table" and moves on 💀).
• do_mapping — maps fastqfile to reference. the options used for mapping are: -r -1 -x -y 0.96 🔥

for more info on the mapping and indexing options we just talked about, go read the SMALT manual, it's at ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf — yes it's an ftp link, we don't question the ancestors 🫶

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👑 AUTHOR 👑

Carla Cummins <path-help@sanger.ac.uk> — thank you for your service, queen 🫡💜

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⭐ COPYRIGHT AND LICENSE ⭐

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

it's free software, licensed under:

The GNU General Public License, Version 3, June 2007

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and that's the whole page bestie!! this was perl v5.30.0, dated 2020-01-11, and it's the Bio::Tradis::Map(3pm) manpage — go forth and map some reads, you're gonna slay 🌸💅✨🦋