bcalm - de Bruijn compaction in low memory
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']
This manpage was written by Shayan Doust for the Debian
distribution and can be used for any other usage of the program.