NAME

       mapsembler2_kissreads - manual page for mapsembler2_kissreads 2.2.4+dfsg

DESCRIPTION

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

       SYNOPSIS     ./kissreads/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 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  mapsembler2_kissreads  is maintained as a Texinfo manual.  If the info and
       mapsembler2_kissreads programs are properly installed at your site, the command

              info mapsembler2_kissreads

       should give you access to the complete manual.

mapsembler2_kissreads 2.2.4+dfsg                 September 2017                         MAPSEMBLER2_KISSREADS(1)