.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH MINIA "1" "January 2019" "minia 3.2.0" "User Commands"
.SH NAME
minia \- short-read biological sequence assembler
.SH DESCRIPTION
Specifiy \fB\-in\fR
.PP
[minia options]
.IP
[assembly options]
.TP
\fB\-in\fR
(1 arg) :    input reads (fasta/fastq/compressed) or hdf5 file  [default '']
.TP
\fB\-keep\-isolated\fR (0 arg) :
keep short (<= max(2k, 150 bp)) isolated output sequences
.TP
\fB\-traversal\fR
(1 arg) :    traversal type ('contig', 'unitig')  [default 'contig']
.TP
\fB\-fasta\-line\fR
(1 arg) :    number of nucleotides per line in fasta output (0 means one line)  [default '0']
.IP
[graph simplifications options]
.TP
\fB\-no\-bulge\-removal\fR
(0 arg) :    ask to not perform bulge removal
.TP
\fB\-no\-tip\-removal\fR
(0 arg) :    ask to not perform tip removal
.TP
\fB\-no\-ec\-removal\fR
(0 arg) :    ask to not perform erroneous connection removal
.TP
\fB\-tip\-len\-topo\-kmult\fR
(1 arg) :    remove all tips of length <= k * X bp  [default '2.500000']
.TP
\fB\-tip\-len\-rctc\-kmult\fR
(1 arg) :    remove tips that pass coverage criteria, of length <= k * X bp  [default '10.000000']
.TP
\fB\-tip\-rctc\-cutoff\fR
(1 arg) :    tip relative coverage coefficient: mean coverage of neighbors >  X * tip coverage  [default '2.000000']
.TP
\fB\-bulge\-len\-kmult\fR
(1 arg) :    bulges shorter than k*X bp are candidate to be removed  [default '3.000000']
.TP
\fB\-bulge\-len\-kadd\fR
(1 arg) :    bulges shorter than k+X bp are candidate to be removed  [default '100']
.TP
\fB\-bulge\-altpath\-kadd\fR
(1 arg) :    explore up to k+X nodes to find alternative path  [default '50']
.TP
\fB\-bulge\-altpath\-covmult\fR (1 arg) :
bulges of coverage <= X*cov_altpath will be removed  [default '1']
.TP
\fB\-ec\-len\-kmult\fR
(1 arg) :    EC shorter than k*X bp are candidates to be removed  [default '9.000000']
.TP
\fB\-ec\-rctc\-cutoff\fR
(1 arg) :    EC relative coverage coefficient (similar in spirit as tip)  [default '4.000000']
.TP
\fB\-no\-mphf\fR
(0 arg) :    don't construct the MPHF
.IP
[kmer count options]
.TP
\fB\-kmer\-size\fR
(1 arg) :    size of a kmer  [default '31']
.TP
\fB\-abundance\-min\fR
(1 arg) :    min abundance threshold for solid kmers  [default '2']
.TP
\fB\-abundance\-max\fR
(1 arg) :    max abundance threshold for solid kmers  [default '2147483647']
.TP
\fB\-abundance\-min\-threshold\fR
(1 arg) :    min abundance hard threshold (only used when min abundance is "auto")  [default '2']
.TP
\fB\-histo\-max\fR
(1 arg) :    max number of values in kmers histogram  [default '10000']
.TP
\fB\-solidity\-kind\fR
(1 arg) :    way to compute counts of several files (sum, min, max, one, all, custom)  [default 'sum']
.TP
\fB\-solidity\-custom\fR
(1 arg) :    when solidity\-kind is custom, specifies list of files where kmer must be present  [default '']
.TP
\fB\-max\-memory\fR
(1 arg) :    max memory (in MBytes)  [default '5000']
.TP
\fB\-max\-disk\fR
(1 arg) :    max disk   (in MBytes)  [default '0']
.TP
\fB\-solid\-kmers\-out\fR
(1 arg) :    output file for solid kmers (only when constructing a graph)  [default '']
.TP
\fB\-out\fR
(1 arg) :    output file  [default '']
.TP
\fB\-out\-dir\fR
(1 arg) :    output directory  [default '.']
.TP
\fB\-out\-tmp\fR
(1 arg) :    output directory for temporary files  [default '.']
.TP
\fB\-out\-compress\fR
(1 arg) :    h5 compression level (0:none, 9:best)  [default '0']
.TP
\fB\-storage\-type\fR
(1 arg) :    storage type of kmer counts ('hdf5' or 'file')  [default 'hdf5']
.TP
\fB\-histo2D\fR
(1 arg) :    compute the 2D histogram (with first file = genome, remaining files = reads)  [default '0']
.TP
\fB\-histo\fR
(1 arg) :    output the kmer abundance histogram  [default '0']
.IP
[kmer count, advanced performance tweaks options]
.TP
\fB\-minimizer\-type\fR
(1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']
.TP
\fB\-minimizer\-size\fR
(1 arg) :    size of a minimizer  [default '10']
.TP
\fB\-repartition\-type\fR (1 arg) :
minimizer repartition (0=unordered, 1=ordered)  [default '0']
.IP
[bloom options]
.TP
\fB\-bloom\fR
(1 arg) :    bloom type ('basic', 'cache', 'neighbor')  [default 'neighbor']
.TP
\fB\-debloom\fR
(1 arg) :    debloom type ('none', 'original' or 'cascading')  [default 'cascading']
.TP
\fB\-debloom\-impl\fR (1 arg) :
debloom impl ('basic', 'minimizer')  [default 'minimizer']
.IP
[branching options]
.TP
\fB\-branching\-nodes\fR (1 arg) :
branching type ('none' or 'stored')  [default 'stored']
.TP
\fB\-topology\-stats\fR
(1 arg) :    topological information level (0 for none)  [default '0']
.IP
[general options]
.TP
\fB\-config\-only\fR
(0 arg) :    dump config only
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores  [default '0']
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-integer\-precision\fR (1 arg) :
integers precision (0 for optimized value)  [default '0']
.TP
[debug
options]
.TP
\fB\-redo\-bcalm\fR
(0 arg) :    debug function, redo the bcalm algo
.TP
\fB\-skip\-bcalm\fR
(0 arg) :    same, but       skip     bcalm
.TP
\fB\-redo\-bglue\fR
(0 arg) :    same, but       redo     bglue
.TP
\fB\-skip\-bglue\fR
(0 arg) :    same, but       skip     bglue
.TP
\fB\-redo\-links\fR
(0 arg) :    same, but       redo     links
.TP
\fB\-skip\-links\fR
(0 arg) :    same, but       skip     links
.TP
\fB\-nb\-glue\-partitions\fR (1 arg) :
number of glue partitions (automatically calculated by default)  [default '0']
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.