BCALM(1)

okay so bestie, you've landed on BCALM(1), the User Commands page for bcalm ✨ it's a de Bruijn graph tool, it's giving bioinformatics main character energy, and I'm gonna walk you through every single flag like we're texting at 2am 💖

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🌸 NAME 🌸

bcalm — de Bruijn compaction in low memory 🧬💅

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✨ DESCRIPTION ✨

It's a Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. That's the whole vibe. No cap. 🦋

Here's how you actually call it, and yes the invocation line is literally just the binary plus options:

[bcalm_1 options]

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🎀 [bcalm_1 options] 🎀

• -nb-cores (1 arg) — number of cores 💻 [default '0']
• -verbose (1 arg) — verbosity level 📢 [default '1']
• -version (0 arg) — version 🏷️
• -help (0 arg) — help 🙋

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🧬 [graph options] 🧬

• -no-mphf (0 arg) — don't construct the MPHF 🚫 [no default given, it's just off unless you say it]

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🔢 [kmer count options] 🔢

• -in (1 arg) — reads file 📂 [default '']
• -kmer-size (1 arg) — size of a kmer 📏 [default '31']
• -abundance-min (1 arg) — min abundance threshold for solid kmers 🌱 [default '2']
• -abundance-max (1 arg) — max abundance threshold for solid kmers 🚀 [default '2147483647']
• -solidity-custom (1 arg) — when solidity-kind is custom, specifies list of files where kmer must be present 🗂️ [default '']
• -max-memory (1 arg) — max memory (in MBytes) 🧠 [default '5000']
• -max-disk (1 arg) — max disk (in MBytes) 💾 [default '0']
• -out (1 arg) — output file 📤 [default '']
• -out-dir (1 arg) — output directory 📁 [default '.']
• -out-tmp (1 arg) — output directory for temporary files 🗃️ [default '.']
• -out-compress (1 arg) — h5 compression level (0:none, 9:best) 🗜️ [default '0']
• -storage-type (1 arg) — storage type of kmer counts ('hdf5' or 'file') 🧊 [default 'hdf5']
• -histo2D (1 arg) — compute the 2D histogram (with first file = genome, remaining files = reads) 📊 [default '0']
• -histo (1 arg) — output the kmer abundance histogram 📈 [default '0']

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⚡ [kmer count, advanced performance tweaks options] ⚡

these are the deep cuts, the iykyk settings 🫶

• -minimizer-type (1 arg) — minimizer type (0=lexi, 1=freq) 🔍 [default '1']
• -minimizer-size (1 arg) — size of a minimizer 🔬 [default '10']
• -repartition-type (1 arg) — minimizer repartition (0=unordered, 1=ordered) 🔀 [default '1']

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🌸 [bloom options] 🌸

• -bloom (1 arg) — bloom type ('basic', 'cache', 'neighbor') 🌼 [default 'neighbor']
• -debloom (1 arg) — debloom type ('none', 'original' or 'cascading') 🍃 [default 'cascading']
• -debloom-impl (1 arg) — debloom impl ('basic', 'minimizer') 🛠️ [default 'minimizer']

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🌿 [branching options] 🌿

• -branching-nodes (1 arg) — branching type ('none' or 'stored') 🌳 [default 'stored']
• -topology-stats (1 arg) — topological information level (0 for none) 📐 [default '0']

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💜 [general options] 💜

• -config-only (0 arg) — dump config only 🗒️
• -nb-cores (1 arg) — number of cores 💻 [default '0']
• -verbose (1 arg) — verbosity level 📢 [default '1']
• -integer-precision (1 arg) — integers precision (0 for optimized value) 🔢 [default '0']

bestie yes, -nb-cores and -verbose show up in both [bcalm_1 options] and [general options]. That's not a typo on my part, that's literally the page. Not me pointing it out, it's just facts. 💀

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🐛 [debug options] 🐛

these are the developer gremlin buttons, use them when you're debugging and not in production okay 🙈

• -redo-bcalm (0 arg) — debug function, redo the bcalm algo 🔁
• -skip-bcalm (0 arg) — same, but skip bcalm ⏭️
• -redo-bglue (0 arg) — same, but redo bglue 🔁
• -skip-bglue (0 arg) — same, but skip bglue ⏭️
• -redo-links (0 arg) — same, but redo links 🔁
• -skip-links (0 arg) — same, but skip links ⏭️
• -nb-glue-partitions (1 arg) — number of glue partitions (automatically calculated by default) 🧩 [default '0']

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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. iconic behaviour honestly 🫶

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and that's the whole thing, bestie 🌈 this was bcalm 2.2.1, dated September 2019, and this page is filed under BCALM(1) in the User Commands section 💖 go build a compacted de Bruijn graph, you absolute legend ✨🎀