PBSIM(1)

💖 PBSIM(1) 💖

okay bestie, welcome to the pbsim manual page — section 1, the real one, the iconic one. pull up a chair, grab a boba, we're simulating PacBio reads together 🧚✨

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🌸 NAME 🌸

pbsim — a simulator for PacBio sequencing reads. yes she's a simulator. yes she's serving. 🎀

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🦋 SYNOPSIS 🦋

pbsim [options] <reference.fasta>

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✨ DESCRIPTION ✨

so the pbsim command makes simulated PacBio reads for a reference FASTA sequence, which is the <reference.fasta> you hand her. that's the whole gig. she ate. 💅

Model files (aka the parameters for the --model-qc option) live in the /usr/share/pbsim/models directory. they're just sitting there. waiting for you. 🫶

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👑 OPTIONS 👑

the options for pbsim split into three little friend groups: general, sampling-based, and model-based simulation options. let's meet them all, no one gets left out, periodt.

🌈 General options

• --prefix — prefix of output files (sd).
• --data-type — data type. CLR or CCS (CLR).
• --depth — depth of coverage (CLR: 20.0, CCS: 50.0).
• --length-min — minimum length (100).
• --length-max — maximum length (CLR: 25000, CCS: 2500).
• --accuracy-min — minimum accuracy (CLR: 0.75, CCS: fixed as 0.75). heads up bestie, this option can be used only in case of CLR. 🚨
• --accuracy-max — maximum accuracy (CLR: 1.00, CCS: fixed as 1.00). again, this option can be used only in case of CLR.
• --difference-ratio — ratio of differences, in the order substitution:insertion:deletion. each value goes up to 1000 (CLR: 10:60:30, CCS: 6:21:73).
• --seed — for a pseudorandom number generator (Unix time).

🎀 Options for sampling-based simulation

• --sample-fastq — FASTQ format file to sample.
• --sample-profile-id — sample-fastq (filtered) profile ID. when you use --sample-fastq, the profile gets stored, and sample_profile_<ID>.fastq and sample_profile_<ID>_.stats are created. when you're not using --sample-fastq, the profile is re-used instead. and lowkey important: when the profile is used, --length-min,max and --accuracy-min,max would be the same as the profile. so don't fight it, the profile wins. 😭

🧚 Options for model-based simulation

• --model_qc — model of quality code.
• --length-mean — mean of length model (CLR: 3000.0, CCS: 450.0).
• --length-sd — standard deviation of length model (CLR: 2300.0, CCS: 170.0).
• --accuracy-mean — mean of accuracy model (CLR: 0.78, CCS: fixed as 0.98). this option can be used only in case of CLR. 💀
• --accuracy-sd — standard deviation of accuracy model (CLR: 0.02, CCS: fixed as 0.02). also only in case of CLR.

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🔥 EXAMPLES 🔥

to run model-based simulation:

pbsim --data-type CLR \
      --depth 20 \
      --model_qc /usr/share/pbsim/models/model_qc_clr \
      reference.fasta

in the example above, simulated read sequences are randomly sampled from a reference sequence (reference.fasta) and differences (errors) of the sampled reads are introduced. the data type is CLR, and the coverage depth is 20. if the reference sequence is a multi-FASTA file, the simulated data is created for each FASTA. three output files are created for each FASTA, bestie, three:

• sd_0001.ref is a single-FASTA file which is copied from the reference sequence.
• sd_0001.fastq is a simulated read dataset in the FASTQ format.
• sd_0001.maf is a list of alignments between the reference sequence and the simulated reads in the MAF format.

the length and accuracy of reads are simulated based on our model of PacBio read. ✨

to run sampling-based simulation:

pbsim --data-type CLR \
      --depth 20 \
      --sample-fastq sample.fastq \
      reference.fastaq

in the sampling-based simulation, read length and quality score are the same as those of a read taken randomly in the sample PacBio dataset (sample.fastq). like, she literally borrowed it. 🙈

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💜 LICENSE 💜

pbsim is available under the terms of the GNU General Public License, version 2 (GPL-2). slay, legally. ⚖️

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🌟 AUTHORS 🌟

Michiaki Hamada (mhamada@k.u-tokyo.ac.jp), Yukiteru Ono — the icons who built this. 👑

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and that's the whole page, bestie!! this was the pbsim manual, section 1, and the footer says PBSIM(1) — so if you ever forget where you read this, it's the PBSIM(1) page, mwah 💋 go simulate something gorgeous 🦋💖