SPADES(1)

💖 SPADES — bestie's guide to the SPAdes genome assembler 💖

okay so. you found spades, the manual page, and honestly? iconic. this is the main character executable of the whole SPAdes software situation. it takes your genomic reads, assembles them, and drops the resulting assembly into <output_dir>. no cap. let's go 🧚✨

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🌸 SYNOPSIS 🌸

spades [options] -o <output_dir>

that's it. that's the whole vibe. options in, output dir out. 💅

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🦋 DESCRIPTION 🦋

spades is the main executable for the SPAdes software, fr fr. it assembles the genomic reads you hand it and places the resulting assembly in <output_dir>. like a little assembly fairy but make it bioinformatics 🧬✨

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✨ OPTIONS ✨

🎀 Basic options

• -o <output_dir> — the directory where all the resulting files go. this one is required, bestie, don't skip it 🙈
• --sc — this flag is required for MDA (single-cell) data 👑
• --meta — this flag is required for metagenomic sample data 🦠
• --rna — this flag is required for RNA-seq data 🧬
• --plasmid — runs the plasmidSPAdes pipeline for plasmid detection 💫
• --iontorrent — this flag is required for IonTorrent data ⚡
• --test — runs SPAdes on a toy dataset 🧸 (yes, toy. adorable.)
• -h/--help — prints this usage message. hi, hello, welcome 💖

🌈 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 <#> (<#> = 1,2,3,4,5)
• --pe<#>-1 <filename> — file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
• --pe<#>-2 <filename> — file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
• --pe<#>-s <filename> — file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
• --pe<#>-<or> — orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
• --s<#> <filename> — file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
• --mp<#>-12 <filename> — file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
• --mp<#>-1 <filename> — file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
• --mp<#>-2 <filename> — file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
• --mp<#>-s <filename> — file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
• --mp<#>-<or> — orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
• --hqmp<#>-12 <filename> — file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
• --hqmp<#>-1 <filename> — file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
• --hqmp<#>-2 <filename> — file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
• --hqmp<#>-s <filename> — file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
• --hqmp<#>-<or> — orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
• --nxmate<#>-1 <filename> — file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
• --nxmate<#>-2 <filename> — file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
• --sanger <filename> — file with Sanger reads
• --pacbio <filename> — file with PacBio reads
• --nanopore <filename> — file with Nanopore reads
• --trusted-contigs <filename> — file with trusted contigs 🫶
• --untrusted-contigs <filename> — file with untrusted contigs 🙈

💜 Pipeline options

• --only-error-correction — runs only read error correction (no assembling, just the correction era of the pipeline)
• --only-assembler — runs only assembling (no read error correction)
• --careful — tries to reduce the number of mismatches and short indels 🎯
• --continue — continue the run from the last available check-point 🏃♀️
• --restart-from <cp> — restart the run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
• --disable-gzip-output — forces error correction not to compress the corrected reads
• --disable-rr — disables the repeat resolution stage of assembling

⭐ Advanced options

• --dataset <filename> — file with dataset description in YAML format 📄
• -t/--threads <int> — number of threads [default: 16]
• -m/--memory <int> — RAM limit for SPAdes in Gb. if you exceed it, it terminates. not a drill 💀 [default: 250]
• --tmp-dir <dirname> — directory for temporary files [default: <output_dir>/tmp]
• -k <int,int,...> — comma-separated list of k-mer sizes. must be odd and less than 128, lowkey important 🔥 [default: 'auto']
• --cov-cutoff <float> — coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
• --phred-offset <33 or 64> — PHRED quality offset in the input reads (33 or 64) [default: auto-detect] 👀

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ngl bestie, double-check your flags before you hit enter. a wrong library number or a missing -o will have you sitting there confused and that's not the energy we're bringing today 🙈💅

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that's the whole page, periodt. 🎀 this was the SPADES(1) manual, and the footer is just more SPADES(1) energy — no version number or date dropped on this one, so that's literally all she wrote. go assemble something gorgeous, bestie, you got this 🦋💖✨