mapsembler2_kissreads - Checks for each sequence contained into the toCheck.fasta if it is read coherent

       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)

       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

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

-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

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]