DWGSIM:(1)

💖 DWGSIM:(1) 💖

okay bestie, pull up a chair, because we're talking about dwgsim — a short read simulator, living in the User Commands section of your friendly neighbourhood manual. yes, the manual name is DWGSIM:(1), and yes it is iconic. ✨

🌸 SYNOPSIS 🌸

dwgsim [options] <in.ref.fa> <out.prefix>

like, give it your reference fasta and a prefix for the output and it just goes. main character energy fr fr.

🦋 DESCRIPTION 🦋

DWGSIM is a short read simulator — it simulates reads from modern sequencing platforms. that's it, that's the vibe. it makes fake reads so you can test your pipeline without actually having to, y'know, sequence anything. 💅

✨ OPTIONS ✨

okay so here's the whole menu, no skips, no cuts, we're doing all of them:

• -e FLOAT — per base/color/flow error rate of the first read. defaults to the range [from 0.020 to 0.020 by 0.000] 🎀
• -E FLOAT — per base/color/flow error rate of the second read. same deal: [from 0.020 to 0.020 by 0.000]
• -i — use the inner distance instead of the outer distance for pairs [False]. not me flipping the whole measurement around 🙈
• -d INT — outer distance between the two ends for pairs [500]
• -s INT — standard deviation of the distance for pairs [50.000]
• -N INT — number of read pairs. (-1 to disable) [-1]
• -C FLOAT — mean coverage across available positions. (-1 to disable) [100.00]
• -1 INT — length of the first read [70]
• -2 INT — length of the second read [70]
• -r FLOAT — rate of mutations [0.0010]
• -F FLOAT — frequency of given mutation, for simulating low fequency somatic mutations [0.5000]. NB: freqeuncy F refers to the first strand of mutation, therefore mutations on the second strand occur with a frequency of 1-F. (yes bestie, we copied the typos verbatim, it's giving authenticity 💀)
• -R FLOAT — fraction of mutations that are indels [0.10]
• -X FLOAT — probability an indel is extended [0.30]
• -I INT — the minimum length indel [1]
• -y FLOAT — probability of a random DNA read [0.05]
• -n INT — maximum number of Ns allowed in a given read [0]
• -c INT — generate reads for [0]: 0: Illumina, 1: SOLiD, 2: Ion Torrent. pick your platform era 🫶
• -S INT — generate reads [0]: 0: default (opposite strand for Illumina, same strand for SOLiD/Ion Torrent), 1: same strand (mate pair), 2: opposite strand (paired end)
• -f STRING — the flow order for Ion Torrent data [(null)]
• -B — use a per-base error rate for Ion Torrent data [False]
• -H — haploid mode [False]
• -z INT — random seed (-1 uses the current time) [-1]
• -M — generate a mutations file only [False]
• -m FILE — the mutations txt file to re-create [not using]
• -b FILE — the bed-like file set of candidate mutations [(null)]
• -v FILE — the vcf file set of candidate mutations (use pl tag for strand) [(null)]
• -x FILE — the bed of regions to cover [not using]
• -P STRING — a read prefix to prepend to each read name [not using]
• -q STRING — a fixed base quality to apply (single character) [not using]
• -Q FLOAT — standard deviation of the base quality scores [2.00]
• -s INT — standard deviation of the distance for pairs [50.000] — yes, this one is listed twice in the original and we are not judging, we are just reporting the facts, periodt 💜
• -h — print this message

🎀 Note: For SOLiD mate pair reads and BFAST, the first read is F3 and the second is R3. For SOLiD mate pair reads and BWA, the reads in the first file are R3, the reads annotated as the first read etc.

🌈 Note: The longest supported insertion is 4294967295. that is a very long insertion bestie, don't push it.

and that's the whole page, no cap. go simulate some reads, you got this. 👑

this little masterpiece is dwgsim: 0.1.11, dated September 2015, and it lives at DWGSIM:(1) — slay, drink water, bye 💖✨