LAMASSEMBLE(1)

💖 LAMASSEMBLE(1) 💖

User Commands · the lamassemble era 🧬✨

✨ NAME ✨

lamassemble — merges overlapping "long" DNA reads into a consensus sequence 🧬💅

🌸 SYNOPSIS 🌸

lamassemble [options] last-train.out sequences.fx > consensus.fa

🦋 DESCRIPTION 🦋

Merge DNA sequences into a consensus sequence. That's it, that's the whole vibe. 🫶

👑 OPTIONS 👑

okay bestie, here's the whole menu, no skips, we're reading every single one:

• -h, --help — show this help message and exit 💖
• -a, --alignment — print an alignment, not a consensus ✨
• -c, --consensus — just make a consensus, of already-aligned sequences 🎀
• -g G, --gap-max=G — use alignment columns with <= G% gaps (default=50) 🌸
• --end — ... including gaps past the ends of the sequences 🦋
• -s S, --seq-min=S — omit consensus flanks with < S sequences (default=1) 💜
• -n NAME, --name=NAME — name of the consensus sequence (default=lamassembled) ⭐
• -o BASE, --out=BASE — just write MAFFT input files, named BASE.xxx 💅
• -p P, --prob=P — use pairwise restrictions with error probability <= P (default=0.002) 🔥
• -d D, --diagonal-max=D — max change in alignment diagonal between pairwise alignments (default=1000) 🌈
• -v, --verbose — show progress messages 👀
• --all — use all of each sequence, not just aligning part 🫶
• --mafft=ARGS — additional arguments for MAFFT 😭

💀 LAST options 💀

not me sneaking a whole other option family in here, but fr fr these are the LAST ones:

• -P P — number of parallel threads (default=1) 🧚
• -W W — use minimum positions in length-W windows (default=19) 🍓
• -m M — max initial matches per query position (default=5) 💖
• -z Z — max gap length (default=30) 🌸

that's the whole page, bestie, you ate it 💅✨

this was lamassemble version 1.4.2, from July 2022 — iconic behavior, no cap 🎀🦋