Provided by: minia_3.2.6-4build2_amd64 bug

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.