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MINIA(1) User Commands MINIA(1)

NAME

minia - short-read biological sequence assembler

DESCRIPTION

Specifiy -in

[minia options]

[assembly options]
(1 arg) : input reads (fasta/fastq/compressed) or hdf5 file [default '']
keep short (<= max(2k, 150 bp)) isolated output sequences
(1 arg) : traversal type ('contig', 'unitig') [default 'contig']
(1 arg) : number of nucleotides per line in fasta output (0 means one line) [default '0']
[graph simplifications options]
(0 arg) : ask to not perform bulge removal
(0 arg) : ask to not perform tip removal
(0 arg) : ask to not perform erroneous connection removal
(1 arg) : remove all tips of length <= k * X bp [default '2.500000']
(1 arg) : remove tips that pass coverage criteria, of length <= k * X bp [default '10.000000']
(1 arg) : tip relative coverage coefficient: mean coverage of neighbors > X * tip coverage [default '2.000000']
(1 arg) : bulges shorter than k*X bp are candidate to be removed [default '3.000000']
(1 arg) : bulges shorter than k+X bp are candidate to be removed [default '100']
(1 arg) : explore up to k+X nodes to find alternative path [default '50']
bulges of coverage <= X*cov_altpath will be removed [default '1']
(1 arg) : EC shorter than k*X bp are candidates to be removed [default '9.000000']
(1 arg) : EC relative coverage coefficient (similar in spirit as tip) [default '4.000000']
(0 arg) : don't construct the MPHF
[kmer count options]
(1 arg) : size of a kmer [default '31']
(1 arg) : min abundance threshold for solid kmers [default '2']
(1 arg) : max abundance threshold for solid kmers [default '2147483647']
(1 arg) : min abundance hard threshold (only used when min abundance is "auto") [default '2']
(1 arg) : max number of values in kmers histogram [default '10000']
(1 arg) : way to compute counts of several files (sum, min, max, one, all, custom) [default 'sum']
(1 arg) : when solidity-kind is custom, specifies list of files where kmer must be present [default '']
(1 arg) : max memory (in MBytes) [default '5000']
(1 arg) : max disk (in MBytes) [default '0']
(1 arg) : output file for solid kmers (only when constructing a graph) [default '']
(1 arg) : output file [default '']
(1 arg) : output directory [default '.']
(1 arg) : output directory for temporary files [default '.']
(1 arg) : h5 compression level (0:none, 9:best) [default '0']
(1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5']
(1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default '0']
(1 arg) : output the kmer abundance histogram [default '0']
[kmer count, advanced performance tweaks options]
(1 arg) : minimizer type (0=lexi, 1=freq) [default '0']
(1 arg) : size of a minimizer [default '10']
minimizer repartition (0=unordered, 1=ordered) [default '0']
[bloom options]
(1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor']
(1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading']
debloom impl ('basic', 'minimizer') [default 'minimizer']
[branching options]
branching type ('none' or 'stored') [default 'stored']
(1 arg) : topological information level (0 for none) [default '0']
[general options]
(0 arg) : dump config only
(1 arg) : number of cores [default '0']
(1 arg) : verbosity level [default '1']
integers precision (0 for optimized value) [default '0']
[debug
options]
(0 arg) : debug function, redo the bcalm algo
(0 arg) : same, but skip bcalm
(0 arg) : same, but redo bglue
(0 arg) : same, but skip bglue
(0 arg) : same, but redo links
(0 arg) : same, but skip links
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.

January 2019 minia 3.2.0