DBGH5(1)

🦋 NAME 🦋

hiii bestie, welcome to the manual page for dbgh5, section 1, User Commands — yes it's giving big brain energy 💅✨

dbgh5 — builds a DeBruijn graph from a set of reads and saves it as a HDF5 file. that's the whole point of the girl, okay? 🎀

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🌸 DESCRIPTION 🌸

under the hood it's all gatb-core-library 🫶

version — 1.4.1 (the icon, the moment, the era) 👑

build_kmer_size — 32 64 96 128 (those are the sizes it was built for, periodt)

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🧚 graph options

• -no-mphf (0 arg) — don't construct the MPHF. that's it, that's the option, she said no 💅

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🍓 kmer count options

• -in (1 arg) — reads file 📖
• -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']
• -abundance-min-threshold (1 arg) — min abundance hard threshold (only used when min abundance is "auto") [default '2']
• -histo-max (1 arg) — max number of values in kmers histogram [default '10000']
• -solidity-kind (1 arg) — way to compute counts of several files (sum, min, max, one, all, custom) [default 'sum']
• -solidity-custom (1 arg) — when solidity-kind is cutom, 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']
• -solid-kmers-out (1 arg) — output file for solid kmers (only when constructing a graph) [default '']
• -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']

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🌈 kmer count, algorithmic options options

(yes the heading says "options options", she's extra like that, we love her 💜)

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

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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']
• -email (1 arg) — send statistics to the given email address [default '']
• -email-fmt (1 arg) — 'raw' or 'xml' [default 'raw']
• -check (1 arg) — check result with previous result [default '']
• -check-dump (1 arg) — dump some properties of the created graph into a file [default '']

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💀 debug options

these are debug girlies, don't come for them unless you know what you're doing 🙈

• -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

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💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you king, the dedication is real 🫶✨

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okay that's the whole page, and before you go — this masterpiece is dbgh5 version 1.4.1, dated May 2018, filed under DBGH5(1). it ate and left no crumbs, fr fr 💅👑🎀