ABACAS(1)

🎀 ABACAS(1) — User Commands 🎀

✨ NAME ✨

abacas 💖 okay so this is the one: Algorithm Based Automatic Contiguation of Assembled Sequences 🧚

💅 SYNOPSIS 💅

Okay bestie, there are two ways to call this thing 🫶

abacas -r ref -q qs -p prog  [OPTIONS]

OR

abacas -r ref -q psf -e

Here's what the bits mean 🌸

• ref — a reference sequence, in a single fasta file 📄
• qs — your contigs, in multi-fasta format, plus the MUMmer program you want to use: nucmer or promer 🦋
• psf — a pseudomolecule/ordered sequence file in fasta format 👑

OPTIONS 💜

• -h — print usage 🙈
• -d — use default nucmer/promer parameters ✨
• -s int — minimum length of exact matching word (nucmer default = 12, promer default = 4) 🔥
• -m — print ordered contigs to file in multifasta format 🍓
• -b — print contigs in bin to file 🌈
• -N — print a pseudomolecule without "N"s 💀
• -i int — minimum percent identity [default 40] 💖
• -v int — minimum contig coverage [default 40] 🎀
• -V int — minimum contig coverage difference [default 1] 🌸
• -l int — minimum contig length [default 1] ⭐
• -t — run tblastx on contigs that are not mapped 🧚
• -g string (file name) — print uncovered regions (gaps) on reference to file name 🦋
• -a — append contigs in bin to the pseudomolecule 💅
• -o prefix — output files will have this prefix 🫶
• -P — pick primer sets to close gaps 👑
• -f int — number of flanking bases on either side of a gap for primer design (default 350) 😭
• -R int — run mummer [default 1, use -R 0 to avoid running mummer] 🌈
• -e — escape contig ordering, i.e. go to primer design 🔥
• -c — reference sequence is circular 🍓

🌸 DESCRIPTION 🌸

Okay so ABACAS is literally built to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs, all based on a reference sequence. It's giving precision 💅✨

ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. Then the output gets processed into a pseudomolecule, taking overlapping contigs and gaps into account 🦋 The way it generates a comparison file you can use to visualize ordered and oriented contigs in ACT is so iconic 🌈 Synteny shows up as red bars, and the colour intensity drops as the percent identity between comparable blocks gets lower 🔥 Info on contigs (orientation, percent identity, coverage, and overlap with other contigs) can also be visualized by loading the outputted feature file into ACT 💜

🎀 AUTHOR 🎀

ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK. 🇬🇧💖

This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (and may be used by others). Huge thanks to Andreas for the page 🫶🧚

Version 1.3.1, dated 2011-02-11. Bye bestie, go slay your assembly 💅🦋🌸