NAME

       kissreads - manual page for kissreads 1.0.1

DESCRIPTION

       This   is   kissreads,  version  1.3.2  -  Copyright  INRIA  -  CeCILL  License  The  command  line  was:
       kissreads/kissreads -h NAME kissReads, version 1.3.2 - Copyright INRIA - CeCILL License

       SYNOPSIS kissreads/kissreads <toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta]  ...]  [-k
       value]  [-c  value]  [-d 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.

       -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)

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

       -s silent mode

       --version get the kissReads version and exit

       -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.

kissreads 1.0.1                                   February 2014                                     KISSREADS(1)