---
name: "minia"
section: "1"
platform: "linux"
package: "minia"
version: "3.2.6-4+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/minia"
---

# minia(1)

short-read biological sequence assembler

## NAME

minia - short-read biological sequence assembler

## DESCRIPTION

Specifiy **-in**

\[minia options\]

-

  \[assembly options\]

- **-in**

  (1 arg) :    input reads (fasta/fastq/compressed) or hdf5 file  \[default ''\]

- **-keep-isolated** (0 arg) :

  keep short (\<= max(2k, 150 bp)) isolated output sequences

- **-traversal**

  (1 arg) :    traversal type ('contig', 'unitig')  \[default 'contig'\]

- **-fasta-line**

  (1 arg) :    number of nucleotides per line in fasta output (0 means one line)  \[default '0'\]

-

  \[graph simplifications options\]

- **-no-bulge-removal**

  (0 arg) :    ask to not perform bulge removal

- **-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 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 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)  \[default '4.000000'\]

- **-no-mphf**

  (0 arg) :    don't construct the MPHF

-

  \[kmer count options\]

- **-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 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)  \[default ''\]

- **-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')  \[default 'hdf5'\]

- **-histo2D**

  (1 arg) :    compute the 2D histogram (with first file = genome, remaining files = reads)  \[default '0'\]

- **-histo**

  (1 arg) :    output the kmer abundance histogram  \[default '0'\]

-

  \[kmer count, advanced performance tweaks options\]

- **-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)  \[default '0'\]

-

  \[bloom options\]

- **-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')  \[default 'minimizer'\]

-

  \[branching options\]

- **-branching-nodes** (1 arg) :

  branching type ('none' or 'stored')  \[default 'stored'\]

- **-topology-stats**

  (1 arg) :    topological information level (0 for none)  \[default '0'\]

-

  \[general options\]

- **-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)  \[default '0'\]

- \[debug

  options\]

- **-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)  \[default '0'\]

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.