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).

kissplice 2.6.7                                    2025-04-30                                       KISSPLICE(1)