minia - short-read biological sequence assembler
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']
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.