KISSNP2(1)

💖 KISSNP2 💖

okay so bestie, welcome to kissnp2, a User Commands girly living in section 1 of the manual. She detects SNPs and indels from read sets and honestly? she ate. 👑

✨ NAME ✨

kissnp2 — detects SNPs and indels from read sets 💅

🌸 DESCRIPTION 🌸

so like, here's the whole vibe. this is [Kissnp2 options] and every single one of them matters, so let's go one by one, no skipping, we're doing the full tour 🎀

• -x (0 arg) — keep truncated bubbles, the ones that have no successors on the 2 paths at the same position 🫧
• -P (1 arg) — maximal number of polymorphism per bubble. default is '1' ✨
• -D (1 arg) — maximal size of a predicted indel. default is '0' 🧬
• -dont_output_first_coverage (0 arg) — Don't output the first coverage threshold. Use this option whent the reference file is used for finding the variants 🙈 (yes that's the spelling, we keep it exactly as-is, character for character, periodt)
• -in (1 arg) — input file (likely a hdf5 file) 📂
• -coverage_file (1 arg) — File (.h5) generated by kissnp2, containing the coverage threshold per read set. default is '_removemeplease' 💀 (iconic default name ngl)
• -out (1 arg) — output name 🏷️
• -T (0 arg) — extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with -t 🚫
• -t (0 arg) — extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with -T 🚫
• -max_symmetrical_crossroads (1 arg) — In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit. default is '-1' 🛣️
• -b (1 arg) — branching mode 🌿
  • 0: forbid SNPs for which any of the two paths is branching (high precision, low recall)
  • 1: forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position (default value)
  • 2: No limitation on branching (low precision, high recall)

default is '1' ⭐

• -max_ambigous_indel (1 arg) — Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output. default is '20' 🌀
• -l (0 arg) — conserve low complexity SNPs 🍓
• -nb-cores (1 arg) — number of cores. default is '0' 🧚
• -verbose (1 arg) — verbosity level. default is '1' 📢
• -version (0 arg) — version 🌈
• -help (0 arg) — help 🆘
• -bfs-max-depth (1 arg) — maximum depth for BFS. default is '200' 🌊
• -bfs-max-breadth (1 arg) — maximum breadth for BFS. default is '20' 🌊

heads up bestie: -T and -t are uncompatible with each other, so don't be messy and try both, okay? 🫶

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 💜

okay that's the whole page, and as a lil sign-off: this is kissnp2 version 2.3.0, dated January 2019, from the kissnp2 2.3.0 source. slay, bye bestie 💖✨🎀🦋