KISSREADS2(1)

🌸 KISSREADS2(1) — User Commands 🌸

okay bestie, sit down, hydrate, and let me tell you about kissreads2 — manual section 1, living in the User Commands corner of the universe. she's the girl who takes your kissnp2 results and makes them even better. iconic behavior honestly. 💅

✨ NAME ✨

kissreads2 — enhances the kissnp2 results by computing per read set. no cap. that's the whole vibe. 🦋

💫 DESCRIPTION 💫

so here's the deal: she takes what kissnp2 gave you and levels it up, working through things per read set. 🫶

the usage shape is basically:

[Kissreads2 options]

and now the options, because that's the main character of this whole page 👑

🎀 the options, one by one, no skips 🎀

• -x (0 arg) — the radseq option: homogeneous read depth along the prediction. ✨
• -predictions (1 arg) — your input predictions.
• -reads (1 arg) — your input reads.
• -unco (1 arg) — the output file name for the uncoherent stuff. default is '/dev/null' (yeah, she'll just throw it away if you don't say otherwise 🙈).
• -co (1 arg) — the output file name for the coherent stuff.
• -hamming (1 arg) — the maximal hamming distance allowed while mapping. default '1'.
• -coverage_file (1 arg) — the .h5 file generated by kissnp2, containing the coverage threshold per read set. default '_removemeplease' 💀
• -k (1 arg) — the size of k, used as the minimal overlap and for kmer spanning read coherence. default '31'.
• -index_stride (1 arg) — the index stride. default '2'.
• -size_seeds (1 arg) — the size of the seeds used (note: this is distinct from the size of k, bestie, don't get it twisted). default '25'.
• -output_fasta (0 arg) — outputs standard Fasta. by default the output is formatted especially for the discoSnp++ pipeline instead.
• -genotype (0 arg) — compute genotypes. 🧬
• -nb-cores (1 arg) — number of cores. default '0'.
• -verbose (1 arg) — verbosity level. default '1'.
• -version (0 arg) — version.
• -help (0 arg) — help.

heads up bestie: -unco defaults to '/dev/null' and -coverage_file defaults to '_removemeplease', so if you don't set those, you're lowkey getting the throwaway behavior. just so you know. 💖

🌈 AUTHOR 🌈

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program too. king behavior honestly 👑

and that's the whole page, bestie 🫶 this was kissreads2 version 2.3.0, dated January 2019 — go slay some read sets for me, mwah 💅✨🎀