RUN_DISCOSNP++.SH(1)

okay bestie, sit down, hydrate, and let me tell you about run_discoSnp++.sh — she's a whole pipeline and she does NOT need a reference genome. periodt. 💖

🌸 NAME 🌸

run_discoSnp++.sh — a pipeline that runs kissnp2 and kissreads together to call SNPs and small indels from NGS reads, with literally no reference genome needed. icon behaviour, truly. 👑

✨ SYNOPSIS ✨

run_discoSnp++.sh -r read_file_of_files [OPTIONS]

💅 DESCRIPTION 💅

So here's the vibe: run_discoSnp++.sh pipelines kissnp2 and kissreads for calling SNPs and small indels from NGS reads, and it does it without the need of a reference genome. We love a self-sufficient queen. 💜

This is Version 2.3.X.

🚨 MANDATORY (like, actually mandatory, do not skip) 🚨

• -r read_file_of_files — the one thing you cannot ghost. Example: -r bank.fof, where bank.fof contains the following two lines:

data_sample/reads_sequence1.fasta
data_sample/reads_sequence2.fasta.gz

🎀 DISCOSNP++ OPTIONS 🎀

• -g — reuse a previously created graph (.h5 file), as long as it's got the same prefix and the same k and c parameters. recycle, but make it science ♻️
• -b value — the branching behaviour setting, choose your fighter:
  • 0: forbid variants for which any of the two paths is branching (high precision, but it lowers the recall in complex genomes). This one is the default value.
  • 1: smart branching — 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).
  • 2: no limitation on branching (lowers the precision, high recall).
• -s value — in b2 mode only: the maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit.
• -D value — discoSnp++ will search for deletions of size from 1 to D included. Default=100.
• -a value — maximal size of ambiguity of INDELs. INDELs whose ambiguity is higher than this value are not output. [default '20']
• -P value — discoSnp++ will search up to P SNPs in a unique bubble. Default=1.
• -p prefix — all out files will start with this prefix. Default="discoRes".
• -l — remove low complexity bubbles. 🧹 bye clutter
• -k value — set the length of used kmers. Must fit the compiled value. Default=31.
• -t — extend found polymorphisms with unitigs. Forced usage when using discoSnpRad.
• -T — extend found polymorphisms with contigs.
• -c value — set the minimal coverage per read set: used by kissnp2 (don't use kmers with lower coverage) and by kissreads (read coherency threshold). This coverage can be automatically detected per read set, or specified per read set — see the documentation. Default=auto.
• -C value — set the maximal coverage for each read set: used by kissnp2 (don't use kmers with higher coverage). Default=2^31-1.
• -d value — set the number of authorized substitutions used while mapping reads on found SNPs (kissreads). Default=1.
• -n — do not compute the genotypes.
• -u — max number of used threads.
• -v — verbose: 0 (avoids progress output) or 1 (enables progress output) -- default=1.

🌈 REFERENCE GENOME AND/OR VCF CREATION OPTIONS 🌈

• -G — reference genome file (fasta, fastq, gzipped or nor). In absence of this file, the VCF created by VCF_creator won't contain mapping related results.
• -R — use the reference file also in the variant calling, not only for mapping results.
• -B — bwa path. e.g. /home/me/my_programs/bwa-0.7.12/ (note that bwa must be pre-compiled). Optional unless option -G is used and bwa is not in the binary path.
• -M — maximal number of mapping errors during BWA mapping phase. Useless unless mapping on reference genome is required (option -G). Default=4.
• -h — prints this message and exist. 💀 (yes, "exist". we don't edit the queen's texts)
• -e — map SNP predictions on reference genome with their extensions. Forced usage when using discoSnpRad.

Any further question: read the readme file or contact us via the Biostar forum: https://www.biostars.org/t/discosnp/ 🫶

🫶 AUTHOR 🫶

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

and that's the whole page, bestie ✨ this was run_discoSnp++.sh version 2.3.0, dated January 2019, and it lives in section RUN_DISCOSNP++.SH(1) — go call some SNPs, no reference required, no cap 💅🦋🌸