NAME

       mapsembler2_kissreads - Checks for each sequence contained into the toCheck.fasta if it is
       read coherent with reads from readsA.fasta or readsB.fasta

SYNOPSIS

       mapsembler2_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 substitution 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

AUTHOR

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