SPRAI(1)

📦 version 0.9.9.23, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SPRAI 💖

okay bestie, gather round, because this is the manual page for SPRAI — single-pass nucleotide sequencing read accuracy improvement — and it's lowkey iconic. it's part of the sprai package, it lives in the General Commands Manual section, and it's about to become your whole personality. no cap.

✨ SYNOPSIS ✨

run it however your little heart desires, bestie:

ezez_vx1 ec.spec {asm.spec | -ec_only} [options]
ezez4qsub_vx1 ec.spec {asm.spec | -ec_only} [options]
ezez4makefile_v4.pl ec.spec [asm.spec] && make -jnproc [ec_only]

like, three whole ways to start the vibe. pick your fighter 💅

🦋 DESCRIPTION 🦋

okay so here's the tea 🍵 Sprai is a tool that corrects sequencing errors in single-pass reads for de novo assembly. it was originally designed to fix sequencing errors in single-molecule DNA sequencing reads, especially the Continuous Long Reads (CLRs) that come out of PacBio RS sequencers. main character energy, honestly.

and now the part that's genuinely important so pay attention bestie: the goal of Sprai is not maximizing the accuracy of error-corrected reads. nope. instead, Sprai is aiming at maximizing the continuity — that is, the N50 contig length — of assembled contigs after error correction. so it's not chasing perfect accuracy, it's chasing long, glorious, continuous contigs. it's giving "bigger picture" ✨

🎀 OPTIONS 🎀

  • -n — shows you the parameters in ec.spec and then dips. just peeks at the config and exits. no work, just vibes.
  • -ec_only — perform error correction only. with this option you do not need to pass in asm.spec, because assembly is not performed at all. correction-only era 🫶
  • -now yyyymmdd_hhmmss — use an existing result_yyyymmdd_hhmmss directory from a previous run, detect the unfinished jobs, and restart at the appropriate stage. it's the "not me picking up exactly where i left off" option 💅

🌈 SEE ALSO 🌈

  • bash5tools(1)

also!! this program is part of sprai. go read the sprai package documentation in /usr/share/doc/sprai, and especially check out the example ec and pbasm spec files in /usr/share/doc/sprai/examples. those example spec files are the blueprint, bestie. iykyk.

reminder that ec.spec is the moment, and asm.spec only joins the party when you're not doing -ec_only. don't forget your yyyymmdd_hhmmss format for -now or it's gonna be awkward 😭

and that's the whole page! this one's dated June 2016 and it's filed as SPRAI(1) — an absolute classic, we stan an aging icon 👑🦋💜

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