kisSplice - local assembly of SNPs, indels and AS events
kissplice [OPTION] [-r READFILES]
Detects alternative splicing events and other kinds of polymorphisms from READFILES (in FASTA or FASTQ format).
- -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.).
- Verbose mode.
- 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).
- Display program's version number and exit.
- Will output the maximum non-ambiguous context of a bubble.
- Will output the id of the nodes composing the two paths of the bubbles.
- Will output the number of branching nodes in each path.
- Keep the node/edges files for all bccs.
- 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 the .counts file after the sequencing-errors-removal step.
- Creates a file with the KissReads mapping information of the reads on the bubbles.
- Execute kissreads in stranded mode.
- Sets the minimum number of reads mapping to a path of a bubble in a read set is needed to call a strand.
- 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 the Type_1 redundant cycles in the result file.
- Keep the low-complexity Type_1 cycles in the result file.
- Cycles with a Shannon entropy value for their upper path below this value will be removed (use --keep-low-complexity to keep them).
- Creates files with informations on compressed redundant cycles.
- Creates a file with informations on removed low-complexity cycles.
- 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).