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.