Provided by: minia_3.2.6-1_amd64 
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.