MINIA

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.