---
name: "kissplice"
section: "1"
platform: "linux"
package: "kissplice"
version: "2.6.7-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kissplice"
---

# kissplice(1)

local assembly of SNPs, indels and AS events

## 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).