FML-ASM(1)

💖 NAME 💖

okay so fml-asm is this little icon that assembles Illumina short reads in small regions ✨ like, it takes your tiny local pile of reads and stitches them into something coherent. it's the fml-asm(1) girlie of the User Commands world and she is serving 🎀

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🌸 SYNOPSIS 🌸

fml-asm [options] <in.fq>

so it's the command, then whatever options you want, then in.fq — your input FASTQ, bestie, and yes it goes at the end, she's the main character of the argument list 👑

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✨ OPTIONS ✨

• -e INT — this is the k-mer length for error correction 🔧. set it to 0 and she'll auto-pick it for you (auto mode ate, no notes), or set it to -1 to just turn error correction off entirely. default is [0].
• -c INT1[,INT2] — the range of k-mer & read count thresholds for ec and graph cleaning 🧼✨. default is [4,8], and yeah you can give it just INT1 or the whole INT1,INT2 duo.
• -l INT — min overlap length during the initial assembly 🧩. default [33].
• -r FLOAT — drop an overlap if its length is below maxOvlpLen*FLOAT 💀 like if it's too short it's getting ghosted, sorry. default [0.7].
• -t INT — number of threads, go off 🚀. default [1]. but fr — don't use multi-threading for small data sets, it's not worth it, she said what she said.
• -d INT — retain a bubble if one side is longer than the other side by more than INT-bp 🫧. default [50].
• -A — discard heterozygotes 🚫🧬. apply this to assemble bacterial genomes, that's literally the whole point of it. also heads up: this overrides -O, so the aggressive tip trimming choice gets overruled, periodt.
• -O — don't apply aggressive tip trimming ✂️ the tips are safe, no cap.
• -g — output the assembly graph in the GFA format 📊 so you can go look at the graph and feel like a scientist.

no DESCRIPTION section in this one bestie, that's just how she is 💅

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that's the whole page 🦋 go assemble something and slay 💜🌸

this was fml-asm version 0.1, dating all the way back to January 2026 — mwah, xoxo, thanks for reading the whole thing, ily bestie 🫶🎀⭐