.TH KISSPLICE "1" "2024-01-09" "kissplice 2.6.2" "User Commands"
.SH NAME
kisSplice \- local assembly of SNPs, indels and AS events
.SH SYNOPSIS
kissplice \-h
.br
kissplice [OPTION] [\-r READFILES]
.SH DESCRIPTION
Detects alternative splicing events and other kinds of polymorphisms from
READFILES (in FASTA or FASTQ format).
.SH OPTIONS
.TP
.B
\-h, \-\-help
Show this help message and exit.
.TP
\fB\-r\fR READFILES
Input fasta/q read files or compressed (.gz) fasta/q files (mutiple, such as "-r file1 -r file2...")
.TP
\fB\-k\fR KVAL
k\-mer size (default=41).
.TP
\fB\-b\fR BVAL
Maximum number of branching nodes (default: 5)
.TP
\fB\-l\fR LLMAX
Maximal length of the shorter path (default: 2k\+1).
.TP
\fB\-m\fR LL_MIN
Minimum length of the shorter path (default 2k\-8).
.TP
\fB\-M\fR UL_MAX
Maximum length of the longest path (default: 1000000),
skipped exons longer than UL_MAX are not reported.
.TP
\fB\-g\fR GRAPH_PREFIX
Path and prefix to pre\-built de Bruijn graph (suffixed
by .edges/.nodes) if jointly used with \fB\-r\fR, graph used
to find bubbles and reads used for quantification.
.TP
\fB\-o\fR OUT_DIR
Path to store the results (default = ./results).
.TP
\fB\-d\fR PATH_TO_TMP
Specific directory (absolute path) where to build
temporary files (default temporary directory otherwise).
.TP
\fB\-t\fR NBPROCS
Number of cores (must be <= number of physical cores).
.TP
\fB\-s\fR 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.).
.TP
\fB\-v\fR
Verbose mode.
.TP
\fB\-u\fR
Keep the nodes/edges file for unfinished bccs.
.TP
\fB\-c\fR MIN_COV
Discard k\-mers tha are present strictly less than this
number of times in the dataset.
(default 2).
.TP
\fB\-C\fR MIN_RELATIVE_COV
Discard edges with relative coverage
below MIN_RELATIVE_COV expressed as a percentage in [0,1).
(default 0.05).
.TP
\fB\-e\fR MIN_EDIT_DIST
Classify as inexact repeats those bubbles whose paths'
edit distance is smaller than MIN_EDIT_DIST
(default 3).
.TP
\fB\-y\fR MAX_CYCLES
Maximal number of bubble enumerations in each bcc. If
exceeded, no bubble is output for the bcc (default:
100000000).
.TP
\fB\-\-mismatches\fR 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 \fB\-\-counts\fR think of increasing min_overlap too.
.TP
\fB\-\-counts\fR COUNTS_TYPE
Changes how the counts will be reported. If 0:
total counts, if 1: counts on junctions, if 2 (default): all counts.
.TP
\fB\-\-min_overlap\fR MIN_OVERLAP
Sets how many nt must overlap a junction to be counted by --counts option (default: 5).
.TP 
\fB\-\-timeout\fR 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).
.TP
\fB\-\-version\fR
Display program's version number and exit.
.TP 
\fB\-\-output-context\fR 
Will output the maximum non-ambiguous context of a bubble.
.TP 
\fB\-\-output-path\fR
Will output the id of the nodes composing the two paths 
of the bubbles.
.TP
\fB\-\-output-branch-count\fR
Will output the number of branching nodes in each path.
.TP
\fB\-\-keep-bccs\fR
Keep the node/edges files for all bccs.
.TP
\fB\-\-not-experimental\fR
Do not use a new experimental algorithm that searches for bubbles by listing all paths.
.TP
\fB\-\-max-memory MAX_MEMORY\fR
If you use the experimental algorithm, you must provide the maximum size of the process's virtual memory (address space) in megabytes (default unlimited).
.TP
\fB\-\-keep-counts\fR
Keep the .counts file after the sequencing-errors-removal step.
.TP
\fB\-\-get-mapping-info\fR
Creates a file with the KissReads mapping information of the reads on the bubbles.
.TP
\fB\-\-stranded\fR
Execute kissreads in stranded mode.
.TP
\fB\-\-strandedAbsoluteThreshold\fR
Sets the minimum number of reads mapping to a path of a bubble in a read set is needed to call a strand.
.TP
\fB\-\-strandedRelativeThreshold\fR
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).
.TP
\fB\-\-keep-redundancy\fR
Keep the Type_1 redundant cycles in the result file.
.TP
\fB\-\-keep-low-complexity\fR
Keep the low-complexity Type_1 cycles in the result file.
.TP
\fB\-\-lc-entropy-threshold\fR
Cycles with a Shannon entropy value for their upper path below this value will be removed (use --keep-low-complexity to keep them).
.TP
\fB\-\-get-redundance-info\fR
Creates files with informations on compressed redundant cycles.
.TP
\fB\-\-get-low-complexity-info\fR
Creates a file with informations on removed low-complexity cycles.
.TP
\fB\-\-type1-only\fR
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).