MEGAHIT_CORE_POPCNT(1)

💖 MEGAHIT_CORE_POPCNT 💖

okay so bestie, this is the manual for megahit_core_popcnt — and no cap, it's an ultra-fast and memory-efficient meta-genome assembler. it's giving main character energy in the metagenomics world, fr fr. ✨

✨ SYNOPSIS ✨

megahit_core_popcnt <sub_program> [sub options]

so like… you call it with a sub_program and then whatever sub options that lil guy needs. that's the whole vibe. 💅

🌸 DESCRIPTION 🌸

okay so this thing is basically a whole toolbox, and each tool is a sub-program. here's the lineup, bestie — every single one, no skips: 🫶

sub-programs

• assemble — assemble from SdBG. it's literally assembling, iykyk 🧚
• local — local asssembly (yes that's spelled "asssembly" in the original, we don't fix, we don't touch, we simply respect it 💀)
• iterate — extract iterative edges. obsessed with how it just… iterates. 👑
• buildlib — build read library. gotta have the library, periodt. 📚
• count — kmer counting. counting them kmers like it's nothing 🔥
• read2sdbg — build sdbg from reads. reads go in, sdbg comes out 🌈
• seq2sdbg — build sdbg from megahit contigs + edges. contigs and edges, the duo 💜
• contig2fastg — convert MEGAHIT's k*.contigs.fa to fastg format. glow-up: fastg edition ✨
• readstat — calculate read stats (# of reads, bases, longest, shortest, average). it knows everything about your reads, lowkey nosy 🍓
• filterbylen — filter contigs by length. short ones, we're so sorry bestie, it's not you it's the length 🙈
• checkcpu — check whether the run-time CPU supports POPCNT and BMI2. a whole vibe check for your CPU 💅
• checkpopcnt — check whether the run-time CPU supports POPCNT. just the POPCNT part of the vibe check 🎀
• checkbmi2 — check whether the run-time CPU supports BMI2. and here's the BMI2 half 🦋
• dumpversion — dump version. it says the version, that's it, that's the whole job 😭
• kmax — the largest k value supported. the biggest k, the ceiling, the limit, the moment 👑

💜 AUTHOR 💜

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

bestie reminder: this is megahit_core_popcnt 1.2.8, dated October 2019 🌸 — so it's a lil vintage, but it still ate and left no crumbs. mwah, go assemble something iconic 💅✨🦋