RNASPADES(1)

📦
version 3.15.5 · 4 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 RNASPADES(1) — the manual page, but make it cute 💖

okay bestie, welcome to RNASPADES(1), the man page for rnaspades — the SPAdes genome assembler running in rnaSPAdes mode. yes that's a lot of "RNA" and "SPAdes" in one sentence, we move. 🧬✨

🌸 NAME 🌸

rnaspades — SPAdes genome assembler (rnaSPAdes mode). that's the whole name section, she's short and she knows it 💅

🦋 SYNOPSIS 🦋

rnaspades [options] -o <output_dir>

that's the vibe. options go in, output dir comes out. periodt.

✨ DESCRIPTION ✨

so basically rnaspades runs SPAdes in rnaSPAdes mode. that's it, that's the description, the original said one sentence and honestly? iconic restraint. no cap. 🫶

🎀 OPTIONS 🎀

💜 Basic options

  • -o <output_dir> — the directory where literally all the resulting files get stored. it is required, so no -o, no party. 🙈
  • --iontorrent — this flag is required if your data is IonTorrent data. don't forget it, bestie, or the data will simply not be understood. 💀
  • --test — runs SPAdes on the toy dataset. perfect for a lil test run before you commit to the real thing. 🧸
  • -h/--help — prints this usage message. the classic. the icon. 🏆

🌈 Input data

  • --12 <filename> — file with interlaced forward and reverse paired-end reads.
  • -1 <filename> — file with forward paired-end reads.
  • -2 <filename> — file with reverse paired-end reads.
  • -s <filename> — file with unpaired reads.
  • --pe<#>-12 <filename> — file with interlaced reads for paired-end library number <#>, where <#> = 1,2,3,4,5. 🍓
  • --pe<#>-1 <filename> — file with forward reads for paired-end library number <#>, where <#> = 1,2,3,4,5.
  • --pe<#>-2 <filename> — file with reverse reads for paired-end library number <#>, where <#> = 1,2,3,4,5.
  • --pe<#>-s <filename> — file with unpaired reads for paired-end library number <#>, where <#> = 1,2,3,4,5.
  • --pe<#>-<or> — orientation of reads for paired-end library number <#>, where <#> = 1,2,3,4,5 and <or> = fr, rf, ff. pick your orientation, she's flexible 💅
  • --s<#> <filename> — file with unpaired reads for single reads library number <#>, where <#> = 1,2,3,4,5.
  • --trusted-contigs <filename> — file with trusted contigs. trust. 🫶
  • --untrusted-contigs <filename> — file with untrusted contigs. no trust. 🙈

🧚 Pipeline options

  • --only-error-correction — runs only read error correction, no assembling. just the glow-up, no photoshoot. ✨
  • --only-assembler — runs only assembling, no read error correction. straight to the main event, no prep. 🔥
  • --continue — continue the run from the last available check-point. she remembers where she left off, queen behavior 👑
  • --restart-from <cp> — restart the run with updated options and from the specified check-point. the check-points are 'ec', 'as', 'k<int>', 'mc'. yes you have to write them exactly like that, character for character, don't get creative bestie. 😭
  • --disable-gzip-output — forces error correction not to compress the corrected reads. uncompressed and unbothered. 💅
  • --disable-rr — disables the repeat resolution stage of assembling. bye bye repeat resolution 🦋

⭐ Advanced options

  • --dataset <filename> — file with a dataset description in YAML format. yaml girlies rise 🌸
  • -t/--threads <int> — number of threads. [default: 16] give her some cores to work with ⚡
  • -m/--memory <int> — RAM limit for SPAdes in Gb, and yes she terminates if exceeded. dramatic? maybe. real? very. [default: 250] 💀
  • --tmp-dir <dirname> — directory for temporary files. [default: <output_dir>/tmp] 🗂️
  • -k <int,int,...> — comma-separated list of k-mer sizes. heads up: they must be odd and less than 128. [default: 'auto'] the k-mer agenda is strict, no even numbers allowed 🎀
  • --cov-cutoff <float> — coverage cutoff value, which can be a positive float number, or 'auto', or 'off'. [default: 'off'] 🌈
  • --phred-offset <33 or 64> — PHRED quality offset in the input reads, either 33 or 64. [default: auto-detect] she'll figure it out herself if you let her 🧚
quick reminder bestie: -o <output_dir> is required, k-mers must be odd and less than 128, and --restart-from only takes 'ec', 'as', 'k<int>', 'mc'. copy those exactly, i'm not playing 💖

and that's the whole page!! thank you for coming to my ted talk, this was the RNASPADES(1) manual page, part of the SPAdes suite, and that little RNASPADES(1) at the very bottom? that's just the page signing off with her own name, as she should. slay, assemble some RNA, drink water 🫶💅✨🌸

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