NAME

       kissplice - detection of polymorphisms in RNA-seq data.

SYNOPSIS

       kissplice -h
       kissplice [OPTION] [-r READFILES]

DESCRIPTION

       Detects  alternative  splicing  events and other kinds of polymorphisms from READFILES (in FASTA or FASTQ
       format).

OPTIONS

       -h, --help
              Show this help message and exit.

       -r READFILES
              Input fasta/q read files (multiple, such as "-r file1 -r file2...").

       -k KVAL
              k-mer size (default=25).

       -l LLMAX
              Maximal length of the shorter path (default: 2k-1).

       -m LL_MIN
              Minimum length of the shorter path (default 2k-8).

       -M UL_MAX
              Maximum length of the longest path (default 1000),  skipped  exons  longer  than  UL_MAX  are  not
              reported.

       -g GRAPH_PREFIX
              Path  and prefix to pre-built de Bruijn graph (suffixed by .edges/.nodes) if jointly used with -r,
              graph used to find bubbles and reads used for quantification.

       -o OUT_DIR
              Path to store the results (default = ./results).

       -d PATH_TO_TMP
              Specific directory (absolute path) where to build temporary  files  (default  temporary  directory
              otherwise).

       -t NBPROCS
              Number of cores (must be <= number of physical cores).

       -s     Don't output SNPs (saves time).

       -v     Verbose mode.

       -u     Keep the nodes/edges file for unfinished bccs.

       -c MIN_COV
              Discard  k-mers  tha are present strictly less than this number of times in the dataset.  (default
              2).

       -C MIN_RELATIVE_COV
              Discard edges with relative coverage below MIN_RELATIVE_COV expressed as a  percentage  in  [0,1).
              (default 0.02).

       -z GENOME_SIZE
              Estimated number of nodes in the De-Bruin Graph.  (default = 1000000000).

       -e MIN_EDIT_DIST
              Classify as inexact repeats those bubbles whose paths' edit distance is smaller than MIN_EDIT_DIST
              (default 3).

       -y MAX_CYCLES
              Maximal number of bubble enumerations in each bcc. If exceeded, no bubble is output  for  the  bcc
              (default 10000).

       --timeout TIMEOUT
              Max  amount of time (in seconds) spent for enumerating bubbles in each bcc. If exceeded, no bubble
              is output for the bcc (default 900).

       --version
              Display program's version number and exit.