SSPACE(1)

🌸 SSPACE — the scaffolding glow-up your contigs have been waiting for

Welcome to the SSPACE(1) manual page bestie, this is the one. Sit down, grab a snack 🍓, we're gonna scaffold some contigs.

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✨ NAME ✨

sspace — the SSPACE-basic scaffolding tool. That's it, that's the name, iconic behavior honestly 👑

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✨ SYNOPSIS ✨

sspace [options] -l [libraryfilename]  -s [contigfilename]

Like, that's the whole vibe. Options in the middle, your library file, your contig file. Boom. Done. 🫶

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✨ DESCRIPTION ✨

Okay so here's the tea 🫖: sspace is a script — yes, a script, not some giant binary — and what it does is extend and scaffold pre-assembled contigs. It does this using one or more mate pairs or paired-end libraries, or honestly even a combination of them. Mix and match, it's flexible like that. 💅

Bestie, please go read the README file at /usr/share/doc/sspace/README.gz for more information. It's giving "required reading" but like, in a cute way. 📖

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✨ OPTIONS ✨

🌟 General Parameters

• -l — Library file containing two paired read files with insert size, error and either mate pair or paired end indication. This one is REQUIRED, no cap, you literally cannot skip it. 🔥
• -s — FASTA file containing contig sequences used for extension. Inserted pairs get mapped to extended and non-extended contigs. Also REQUIRED, bestie, both of these are non-negotiable. 😤
• -x — Indicate whether to extend the contigs of -s using paired reads in -l. Your choices are -x 1 for extension or -x 0 for no extension. Default is -x 0. 🦋

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🧚 Extension Parameters

• -m — Minimum number of overlapping bases with the seed/contig during overhang consensus build up. Default is -m 32. ⭐
• -o — Minimum number of reads needed to call a base during an extension. Default is -o 20. 🌸
• -t — Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension. Default is -t 0. 💀 (exhausted... felt that)
• -u — FASTA/FASTQ file containing unpaired sequence reads. This one is optional, so like, only if you want to. 🙈
• -r — Minimum base ratio used to accept an overhang consensus base. Default is -r 0.9. ✨

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🎀 Scaffolding Parameters

• -z — Minimum contig length used for scaffolding. It filters out contigs below this value. Default is -z 0. 💜
• -k — Minimum number of links (read pairs) to compute scaffold. Default is -k 5. 🔗
• -a — Maximum link ratio between two best contig pairs. Heads up: higher values lead to least accurate scaffolding. Default is -a 0.7. ⚠️
• -n — Minimum overlap required between contigs to merge adjacent contigs in a scaffold. Default is -n 15. 🧬

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🏹 Bowtie Parameters

• -g — Maximum number of allowed gaps during mapping with Bowtie. This corresponds to the -v option in Bowtie. And ngl, a higher number of allowed gaps can lead to least accurate scaffolding. Default is -g 0. 😭
• -T — Specify the number of threads in Bowtie. This corresponds to the -p/--threads option in Bowtie. Default is -T 1. Multithreading era, we love to see it. 🚀

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🌈 Additional Parameters

• -b — Base name for your output files. Default is -b standard_output. Name your babies something cute. 🎀
• -v — Runs in verbose mode. -v 1 for yes, -v 0 for no. Default is -v 0. 👀
• -p — Make a .dot file for visualisation. -p 1 for yes, -p 0 for no. Default is -p 0. Pretty pictures, iykyk. 🖼️

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✨ AUTHORS ✨

Give it up for the icons who made this happen 👑:

• Marten Boetzer
• Walter Pirovano
• Nicola Soranzo

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And that's the whole page bestie!! This was the SSPACE(1) manual page, so if you see SSPACE(1) floating around at the bottom of your terminal, that's just this exact page signing off. Go scaffold something gorgeous. Slay. 💅✨🦋