kissplice(1) 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.