KISSPLICE(1)

📦
version 2.6.7 · 3 versions
, in debian trixie, ubuntu resolute, ubuntu stonking

✨ KISSPLICE(1) ✨

okay bestie, sit down, hydrate, and let me tell you about kisSplice — it's a User Commands situation and it's literally giving 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 🦋

So basically 💖 it detects alternative splicing events and other kinds of polymorphisms from READFILES (which can be in FASTA or FASTQ format, no cap).

👑 OPTIONS 👑

Every single flag, queen. Don't skip, iykyk. 🌈

  • -h, --help — shows this help message and dips out. 🫶
  • -r READFILES — input fasta/q read files, or compressed (.gz) fasta/q files. You can stack them, multiple ones, like "-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, periodt. 🚫
  • -g GRAPH_PREFIX — path and prefix to a pre-built de Bruijn graph (it's suffixed by .edges/.nodes). If you use it jointly with -r, the graph is used to find bubbles and the reads are used for quantification. 🕸️
  • -o OUT_DIR — path to store the results (default = ./results). 📁
  • -d PATH_TO_TMP — specific directory (absolute path, bestie, absolute) where temporary files get built (default is the temporary directory otherwise). 🗂️
  • -t NBPROCS — number of cores. It must be <= number of physical cores. No overcommitting, we're not messy. 💻
  • -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. Like, a lot lot. 😭
  • -v — verbose mode. Spill the tea, program. ☕
  • -u — keep the nodes/edges file for unfinished bccs. 🧺
  • -c MIN_COV — discard k-mers that 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, fr fr. 🔍
  • --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 the --counts option (default: 5). 📎
  • --timeout TIMEOUT — max amount of time (in seconds) spent 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 that 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). 🚀
⚠️ bestie, read that BUT again. Speed comes at a price. 💀

and that's the whole vibe, you're literally a kissSplice expert now 🎀✨

this page is from kissplice 2.6.7, dated 2025-04-30 — mwah, kiss kiss, go assemble something iconic 💖🦋🌸

📦 where this page comes from