NAME

       kissreads - manual page for kissreads 1.2.6

DESCRIPTION

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

       SYNOPSIS  kissreads/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  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 1.2.6                                   November 2014                                     KISSREADS(1)