NAME

       run_discoSnpRad.sh - pipelining kissnp2 and kissreads and clustering per locus for calling
       SNPs and small indels from RAD-seq data without the need of a reference genome

SYNOPSIS

       run_discoSnpRad.sh -r read_file_of_files [OPTIONS]

DESCRIPTION

       run_discoSnpRad.sh, pipelining kissnp2 and kissreads and clustering per locus for  calling
       SNPs  and  small  indels  from RAD-seq data without the need of a reference genome Version
       2.3.X

              MANDATORY:

       -r read_file_of_files
              Example: -r bank.fof with bank.fof containing the two lines

       data_sample/reads_sequence1.fasta
              data_sample/reads_sequence2.fasta.gz

       -S   **absolute**    path    to    short_read_connector    directory,    containing    the
       short_read_connector.sh'' file.
              -Note1:  short read connector must be compiled.  -Note2: if this option is missing,
              discoSnpRad will still however provide a fasta file  containing  SNPs  and  INDELS,
              that won't be clustered by locus

              DISCOSNPRAD OPTIONS:

              -g:  reuse  a previously created graph (.h5 file) with same prefix and same k and c
              parameters.  -b value.

       1: (smart branching) forbid SNPs for which the two paths are branching (e.g. the two paths
       can be created either with a 'A' or a 'C' at the same position Default value
              2: No limitation on branching (lowers the precision, high recall)

              -s value. In b2 mode only: maximal number of symmetrical croasroads traversed while
              trying to close a bubble. Default: no limit -D value. discoSnpRad will  search  for
              deletions  of  size  from  1  to  D included. Default=100 -a value. Maximal size of
              ambiguity of INDELs. INDELS whose ambiguity is  higher  than  this  value  are  not
              output   [default  '20'] -P value. discoSnpRad will search up to P SNPs in a unique
              bubble.  Default=5  -p  prefix.  All  out  files  will  start  with  this   prefix.
              Default="discoRad"  -l:  remove  low complexity bubbles -k value. Set the length of
              used kmers. Must fit the compiled value.  Default=31  -c  value.  Set  the  minimal
              coverage  per  read  set: Used by kissnp2 (don't use kmers with lower coverage) and
              kissreads (read coherency threshold). This coverage can be  automatically  detected
              per  read  set  or  specified  per read set, see the documentation. Default=auto -C
              value. Set the maximal coverage for each read set: Used by kissnp2 (don't use kmers
              with  higher  coverage).  Default=2^31-1  -d  value.  Set  the number of authorized
              substitutions used while mapping reads on found SNPs (kissreads). Default=1 -u: max
              number  of  used  threads  -v:  verbose  0  (avoids  progress output) or 1 (enables
              progress output) -- default=1.

              -h: Prints this message and exist

       Any further question:  read  the  readme  file  or  contact  us  via  the  Biostar  forum:
       https://www.biostars.org/t/discosnp/

AUTHOR

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