---
name: "bcalm"
section: "1"
platform: "linux"
package: "bcalm"
version: "2.2.3-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bcalm"
---

# bcalm(1)

de Bruijn compaction in low memory

## NAME

bcalm - de Bruijn compaction in low memory

## DESCRIPTION

Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

\[bcalm\_1 options\]

- **-nb-cores** (1 arg) :

  number of cores  \[default '0'\]

- **-verbose**

  (1 arg) :    verbosity level  \[default '1'\]

- **-version**

  (0 arg) :    version

- **-help**

  (0 arg) :    help

-

  \[graph options\]

- **-no-mphf**

  (0 arg) :    don't construct the MPHF

-

  \[kmer count options\]

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

-

  \[kmer count, advanced performance tweaks options\]

- **-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)  \[default '1'\]

-

  \[bloom options\]

- **-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 Shayan Doust for the Debian distribution and can be used for any other usage of the program.