NAME

       kisSplice - local assembly of SNPs, indels and AS events

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 or compressed (.gz) fasta/q files (mutiple,  such  as  "-r
              file1 -r file2...")

       -k KVAL
              k-mer size (default=41).

       -b BVAL
              Maximum number of branching nodes (default: 5)

       -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: 1000000), 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 OUTPUT_SNPS
              0, 1 or 2. Changes which types of SNPs will be output. If  0  (default),  will  not
              output  SNPs.  If  1,  will output Type0a-SNPs. If 2, will output Type0a and Type0b
              SNPs (warning: this option may increase a lot the running 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 0.05).

       -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: 100000000).

       --mismatches NB_MISMATCHES
              Maximal number of substitutions authorized between  a  read  and  a  fragment  (for
              quantification  only),  default  2.  If  you increase the mismatch and use --counts
              think of increasing min_overlap too.

       --counts COUNTS_TYPE
              Changes how the counts will be reported. If  0:  total  counts,  if  1:  counts  on
              junctions, if 2 (default): all counts.

       --min_overlap MIN_OVERLAP
              Sets how many nt must overlap a junction to be counted by --counts option (default:
              5).

       --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 100000).

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

       --output-context
              Will output the maximum non-ambiguous context of a bubble.

       --output-path
              Will output the id of the nodes composing the two paths of the bubbles.

       --output-branch-count
              Will output the number of branching nodes in each path.

       --keep-bccs
              Keep the node/edges files for all bccs.

       --not-experimental
              Do  not  use  a new experimental algorithm that searches for bubbles by listing all
              paths.

       --max-memory MAX_MEMORY
              If you use the experimental algorithm, you must provide the  maximum  size  of  the
              process's virtual memory (address space) in megabytes (default unlimited).

       --keep-counts
              Keep the .counts file after the sequencing-errors-removal step.

       --get-mapping-info
              Creates a file with the KissReads mapping information of the reads on the bubbles.

       --stranded
              Execute kissreads in stranded mode.

       --strandedAbsoluteThreshold
              Sets  the  minimum  number  of reads mapping to a path of a bubble in a read set is
              needed to call a strand.

       --strandedRelativeThreshold
              If a strand is called for a path of a bubble in a read set, but the  proportion  of
              reads  calling this strand is less than this threshold, then the strand of the path
              is set to '?' (any strand - not enough evidence to call a strand).

       --keep-redundancy
              Keep the Type_1 redundant cycles in the result file.

       --keep-low-complexity
              Keep the low-complexity Type_1 cycles in the result file.

       --lc-entropy-threshold
              Cycles with a Shannon entropy value for their upper path below this value  will  be
              removed (use --keep-low-complexity to keep them).

       --get-redundance-info
              Creates files with informations on compressed redundant cycles.

       --get-low-complexity-info
              Creates a file with informations on removed low-complexity cycles.

       --type1-only
              Only quantify Type 1 bubbles (alternative splicing events, MAJOR SPEED UP with -b >
              10 BUT all other bubbles will not appear in the result file).