minia - short-read biological sequence assembler

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

minia 3.2.0                                       January 2019                                          MINIA(1)

       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']

       minia - short-read biological sequence assembler