PLASMIDID(1)

💖 NAME 💖

plasmidID — the plasmid identification tool, bestie. it finds plasmids. that's the vibe.

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✨ DESCRIPTION ✨

okay so plasmidID is a computational pipeline that reconstructs and annotates the most likely plasmids hanging out in one single sample 🦋 like it goes in, does its little science dance, and comes back with the plasmids it thinks are actually there.

here's the usage, verbatim, no cap:

usage : ./plasmidID <-1 R1> <-2 R2> <-d database(fasta)> <-s
sample_name> [-g group_name] [options]

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🎀 Mandatory input data 🎀

these ones you cannot skip, queen. no exceptions, no shortcuts.

• -1 | --R1 <filename> — the reads that correspond to paired-end R1. mandatory 🫶
• -2 | --R2 <filename> — the reads that correspond to paired-end R2. mandatory, obviously 💅
• -d | --database <filename> — the database to map and reconstruct against. mandatory 🌸
• -s | --sample <string> — the sample name. mandatory, and heads up: it has to be less than 37 characters. 36 max, bestie, don't test it 😭

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🌈 Optional input data 🌈

these are the little extras, the sprinkles on the cupcake 🧁

• -g | --group <string> — a group name. it's optional! and if you don't set it, all your samples get gathered together in the NO_GROUP group. cozy.
• -c | --contigs <filename> — a file with contigs. if you supply this, plasmidID will not assembly reads. it just skips that whole step 👑
• -a | --annotate <filename> — a file with a configuration file for specific annotation.
• -o <output_dir> — the output directory. by default it's just the current directory, lowkey convenient.

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🔥 Pipeline options 🔥

• --explore — relaxes the default parameters so it can find less reliable relationships within the data supplied and the database. it's giving detective mode 🔍
• --only-reconstruct — the database you supplied will not be filtered, and all sequences will be used as scaffold.

okay important side note: this option does not require R1 and R2. instead, a contig file can be supplied. 💜

• -w — undoes the winner takes it all algorithm when clustering by kmer. this is QUICKER MODE ⚡ periodt.

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💅 Trimming 💅

• --trimmomatic-directory — indicate the directory holding the trimmomatic .jar executable.
• --no-trim — the reads you supplied will not be quality trimmed. raw dogging the data fr fr.

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🌟 Coverage and Clustering 🌟

• -C | --coverage-cutoff <int> — minimum coverage percentage to select a plasmid as scafold (0-100), default 80.
• -S | --coverage-summary <int> — minimum coverage percentage to include plasmids in the summary image (0-100), default 90.
• -f | --cluster <int> — kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5.
• -k | --kmer <int> — identity to filter plasmids from the database with the kmer approach (0-1), default 0.95.

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🦋 Contig local alignment 🦋

• -i | --alignment-identity <int> — minimum identity percentage aligned for a contig to annotate, default 90.
• -l | --alignment-percentage <int> — minimum length percentage aligned for a contig to annotate, default 20.
• -L | --length-total <int> — minimum alignment length to filter blast analysis.
• --extend-annotation <int> — look for annotation over regions with no homology found (base pairs), default 500bp.

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🎨 Draw images 🎨

• --config-directory <dir> — directory holding config files, default config_files/.
• --config-file-individual <file-name> — file name of the individual file used to reconstruct.

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⭐ Additional options ⭐

• -M | --memory <int> — max memory allowed to use.
• -T | --threads <int> — number of threads. give it more, she's hungry 🔥
• -v | --version — version.
• -h | --help — display usage message. bestie behaviour honestly.

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🍓 example 🍓

look at her go:

./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d database.fasta -s ECO_553 -G ENTERO

and another one, with the extra flavour:

./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d PacBio_sample.fasta -c scaffolds.fasta -C 60 -s ECO_60 -G ENTERO --no-trim

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🌸 SEE ALSO 🌸

the full documentation for plasmidID is maintained as a Texinfo manual. if the info and plasmidID programs are properly installed at your site, the command

info plasmidID

should give you access to the complete manual. iykyk 💖

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okay that's the whole page bestie, you're officially plasmid-literate now 👑 this was plasmidID version 1.6.4, dated November 2022 — go reconstruct something iconic, and remember: less than 37 characters on that sample name. mwah 💅✨