MEGAHIT(1)

🌸 MEGAHIT — the ultra-fast, memory-efficient meta-genome assembler 💖

okay bestie, sit down, hydrate, and let me tell you about megahit(1) because this one is literally iconic ✨

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🦋 NAME 🦋

megahit — an ultra-fast and memory-efficient meta-genome assembler. no cap, that's the whole vibe. 🔥

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🎀 DESCRIPTION 🎀

So we're on MEGAHIT v1.2.8, and if you need to slide into someone's inbox about it, the contact is Dinghua Li <voutcn@gmail.com> 💌

✨ Usage: ✨

megahit [options] {-1 <pe1> -2 <pe2> | --12 <pe12> | -r <se>} [-o <out_dir>]

Heads up, bestie: these are the input options you can specify multiple times — and yes, plain text and gz/bz2 extensions are both supported, we love a flexible queen 🫶

• -1 <pe1> — a comma-separated list of fasta/q paired-end #1 files, paired with the files in <pe2> 💅
• -2 <pe2> — a comma-separated list of fasta/q paired-end #2 files, paired with the files in <pe1> ✨
• --12 <pe12> — a comma-separated list of interleaved fasta/q paired-end files 🦋
• -r/--read <se> — a comma-separated list of fasta/q single-end files 🌸

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👑 Optional Arguments 👑

💜 Basic assembly options:

• --min-count <int> — minimum multiplicity for filtering (k_min+1)-mers [2]
• --k-list <int,int,..> — comma-separated list of kmer sizes. every single one must be odd, in the range 15-255, and the increment has to be <= 28. default is [21,29,39,59,79,99,119,141] 💫
• --k-min <int> — minimum kmer size (<= 255), must be an odd number [21]
• --k-max <int> — maximum kmer size (<= 255), must be an odd number [141]
• --k-step <int> — increment of kmer size for each iteration (<= 28), must be an even number [12]

okay wait, there's a whole other way to set --k-list — and it overrides --k-list if either one of them is set. so the trio above (--k-min, --k-max, --k-step) is the alternate route, and they win. iykyk 😌

🌈 Advanced assembly options:

• --no-mercy — do not add mercy kmers. ruthless. 💀
• --bubble-level <int> — intensity of bubble merging (0-2), and 0 disables it entirely [2]
• --merge-level <l,s> — merge complex bubbles of length <= l*kmer_size and similarity >= s [20,0.95]
• --prune-level <int> — strength of low depth pruning (0-3) [2]
• --prune-depth <int> — remove unitigs with avg kmer depth less than this value [2]
• --disconnect-ratio <float> — disconnect unitigs if their depth is less than this ratio times the total depth of itself and its siblings [0.1]
• --low-local-ratio <float> — remove unitigs if their depth is less than this ratio times the average depth of the neighborhoods [0.2]
• --max-tip-len <int> — remove tips less than this value [2*k]
• --cleaning-rounds <int> — number of rounds for graph cleanning [5] (yes, that's how it's spelled in the source, we're keeping it, it's part of the lore 🎀)
• --no-local — disable local assembly 🙈
• --kmin-1pass — use 1pass mode to build the SdBG of k_min ⭐

🧚 Presets parameters:

• --presets <str> — override a whole group of parameters at once. possible values are:
  • meta-sensitive: --min-count 1 --k-list 21,29,39,49,...,129,141
  • meta-large: --k-min 27 --k-max 127 --k-step 10 (this one's for large & complex metagenomes, like soil 🌱)

🖥️ Hardware options:

• -m/--memory <float> — max memory in byte to be used in SdBG construction. if you set it between 0-1, it's treated as a fraction of the machine's total memory [0.9] 💾
• --mem-flag <int> — SdBG builder memory mode. 0: minimum; 1: moderate; others: use all memory specified by -m/--memory [1]
• -t/--num-cpu-threads <int> — number of CPU threads [default is the # of logical processors] ⚡
• --no-hw-accel — run MEGAHIT without BMI2 and POPCNT hardware instructions 🛑

📦 Output options:

• -o/--out-dir <string> — output directory [./megahit_out]
• --out-prefix <string> — output prefix. the contig file will be OUT_DIR/OUT_PREFIX.contigs.fa 📁
• --min-contig-len <int> — minimum length of contigs to output [200]
• --keep-tmp-files — keep all temporary files (your disk said 🫠)
• --tmp-dir <string> — set temp directory

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🌟 Other Arguments 🌟

• --continue — continue a MEGAHIT run from its last available check point. ⚠️ please set the output directory correctly when using this option, bestie, or it's giving chaos 😭
• --test — run MEGAHIT on a toy test dataset 🧸
• -h/--help — print the usage message
• -v/--version — print version

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💌 AUTHOR 💌

This manpage was written by Shayan Doust for the Debian distribution, and can be used for any other usage of the program. periodt. 🫶

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and that's the whole page, bestie — brought to you by megahit 1.2.8, dating all the way back to October 2019 🌸 stay slaying, stay assembling, and remember: the contigs were always going to eat 💅✨