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.

mapsembler2_kissreads 2.2.4                       October 2018                          MAPSEMBLER2_KISSREADS(1)