NAME

       kissreads - manual page for kissreads 1.2.6

DESCRIPTION

       NAME kissReads, version kissreads module 1.2.6 - Copyright INRIA - CeCILL License

       SYNOPSIS     kissreads/kissreads    <toCheck.fasta>    <readsC1.fasta>    [<readsC2.fasta>
       [<readsC3.fasta] ...] [-k value] [-c value] [-d value] [-O value] [-o name] [-u name] [-n]
       [-I] [-i index_stride] [-m align_file] [-s] [-f] [-h]

       DESCRIPTION  Checks  for  each  sequence  contained  into  the toCheck.fasta if it is read
       coherent (each position is covered by at least "min_coverage"  read(s))  with  reads  from
       readsA.fasta or readsB.fasta A sequence s from toCheck is treated as follow:

              if (s coherent with at least one read set): output the sequence as follows

              >original fasta comment|C1:min<avg-corr_avg<max|C2:min<avg-cor_avg<max|C3...: >s

              With  A:min<avg-cor_avg<max  standing  for  :  value of the position having minimal
              coverage in readsA.fasta < average coverage in readsA.fasta - R-squarred  corrected
              average   in  readsA.fa  <  value  of  the  position  having  maximal  coverage  in
              readsA.fasta The coverage is the number of reads that perfectly mapped  a  position
              Any  other  situation  (s  not  coherent  with  any): couple non read coherent, not
              outputed

       OPTIONS

       -k size_seed: will use seeds of length size_seed. Default: 25.

       -O  minimal_read_overlap:  a  read  can  be   mapped   if   its   overlap   is   a   least
              "minimal_read_overlap". Default: k

       -c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2

       -d  max_substitutions:  Maximal  number  of  substitutions authorized between a read and a
              fragment. Note that no substitution  is  allowed  on  the  central  position  while
              anaylizing the kissnp output. Default: 1.

       -o file_name: write read-coherent outputs. Default: standard output

       -u file_name: write unread-coherent outputs. Default: standard output

       -n the input file (toCheck.fasta) is a kissnp output (incompatible with -I option)

              in  this  case: 1/ only the upper characters are considered (no mapping done on the
              extensions) and 2/ the central position (where the SNP occurs) is strictly  mapped,
              no subsitution is authorized on this position.

       -I the input file (toCheck.fasta) is an Intl output (incompatible with -n option)

       -i  index_stride  (int  value).  This  is  a  heuristic for limiting the memory footprint.
              Instead of indexing each kmer of the sequences contained  into  the  toCheck.fasta,
              kissreads  indexes  kmers  occurring  each "index_stride" position. Default = 1 (no
              heuristic)

       -t max number of threads (also limited by number of input files)

       -m align_file, write a file of reads mapped to sequences in file align_file

       -s silent mode

       -f outputs coherent events in a standard fasta file format

       -h prints this message and exit

SEE ALSO

       The full documentation for kissreads is maintained as a Texinfo manual.  If the  info  and
       kissreads programs are properly installed at your site, the command

              info kissreads

       should give you access to the complete manual.