MINIA(1)

💖 NAME 💖

minia — the short-read biological sequence assembler, bestie edition 🧬✨

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✨ DESCRIPTION ✨

okay so listen. minia is a whole assembler and she has OPINIONS, and you gotta tell her what to do. first things first, you specify -in, and then she takes her options in two lil families: the minia options and the assembly options. the synopsis is literally giving:

Specifiy -in

[minia options]

[assembly options]

yes that's how the original spells it, we do not touch the sacred texts 💅

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🎀 [assembly options] 🎀

• -in (1 arg) — your input reads (fasta, fastq, or compressed — she's not picky) or an hdf5 file. [default '']
• -keep-isolated (0 arg) — keep those short isolated output sequences, like, the ones that are <= max(2k, 150 bp). she's little but she's valid 🫶
• -traversal (1 arg) — traversal type, either 'contig' or 'unitig'. [default 'contig']
• -fasta-line (1 arg) — how many nucleotides per line in the fasta output (0 means one single line, no cap). [default '0']

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🌸 [graph simplifications options] 🌸

this is the glow-up section. she's cleaning the graph. unfortunately you can also tell her not to clean it, which is a choice.

• -no-bulge-removal (0 arg) — ask to not perform bulge removal. bulges stay. iconic of them tbh
• -no-tip-removal (0 arg) — ask to not perform tip removal
• -no-ec-removal (0 arg) — ask to not perform erroneous connection removal
• -tip-len-topo-kmult (1 arg) — remove all tips of length <= k * X bp. [default '2.500000']
• -tip-len-rctc-kmult (1 arg) — remove tips that pass the coverage criteria, of length <= k * X bp. [default '10.000000']
• -tip-rctc-cutoff (1 arg) — tip relative coverage coefficient: mean coverage of neighbors > X * tip coverage. [default '2.000000']
• -bulge-len-kmult (1 arg) — bulges shorter than k*X bp are candidate to be removed. [default '3.000000']
• -bulge-len-kadd (1 arg) — bulges shorter than k+X bp are candidate to be removed. [default '100']
• -bulge-altpath-kadd (1 arg) — explore up to k+X nodes to find an alternative path. [default '50']
• -bulge-altpath-covmult (1 arg) — bulges of coverage <= X*cov_altpath will be removed. [default '1']
• -ec-len-kmult (1 arg) — EC shorter than k*X bp are candidates to be removed. [default '9.000000']
• -ec-rctc-cutoff (1 arg) — EC relative coverage coefficient (similar in spirit as tip, so basically the tip energy). [default '4.000000']
• -no-mphf (0 arg) — don't construct the MPHF. just don't. no thoughts, no MPHF

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🦋 [kmer count options] 🦋

counting era. she's counting kmers and she's thriving.

• -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 the 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 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']
• -solid-kmers-out (1 arg) — output file for solid kmers (only when constructing a graph, so don't get your hopes up otherwise). [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, either '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] 🧚

for the girlies who want to go faster 💅

• -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 filter moment, no cap

• -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] ⭐

the main character settings

• -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']

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💀 [debug options] 💀

okay these ones are literally marked as debug, so like, proceed with awareness bestie

• -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 Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

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and that's the whole page bestie!! this is minia 3.2.0 and she's been serving since January 2019 — user commands section 1, a true legend, no notes 💅✨🎀