PBSIM-PacBio-Simulator
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pfaucon
This is an updated mirror of the original PacBio Read Simulator
Hi, Could someone tell me how the error profile is obtained in the model_qc_clr/model_qc_ccs? I'm a beginner in this field and don't know the specific generation steps to generate the...
FYI it appears that the original author has now posted their code on GitHub and have released a version 2 https://github.com/yukiteruono/pbsim2
Hello, Could the software simulate reads with errors which is a long insertion or deletion (length is tens of bases) .
I have a reference sequence (FASTA) that looks like this: ``` >reference_sequence ACTGACTGACTGACTGACTGACTGACTG ACTGACTGACTGACTGACTGACTGACTG ACTGACTGACTGACTGACTGACTGACTG ``` PBSIM included the newlines in the simulated reads. ``` @S1_1 GAAAGCTAAAGATGTTCAGCCAACCATTATTATTAATAAAAATGGCCTTATCTCTTTGGAAGATATCTATGACATTG CGATAAAACAAAAAAAAGTAGAAATATCAACGGAGATCACTGAACTTTTGACGCATGGTCGTGAAAAATTAGAGGAAAAA ``` I...
Hello! I was reading the PBSIM readme page and have a question regarding the following description: ``` To run model-based simulation: pbsim --data-type CLR --depth 20 --model_qc data/model_qc_clr sample/sample.fasta In...
It would be important to know which version of pbsim from the Google Code repo this is based on. I would assume 1.0.3, the most recent version assigned by the...
hi, I saw a preprint article using the latest CCS technology from pacbio.The article is here https://www.biorxiv.org/content/10.1101/519025v2 .Can this tool generate simulation data using the latest error model?If so, how...
I have a question, because I ran the command: `pbsim --data-type CLR --depth 40 --length-min 500 --length-mean 12000 --length-max 40000 --accuracy-min 0.85 --accuracy-mean 0.87 --model_qc /PBSIM-PacBio-Simulator/data/model_qc_clr /path/to/ref.fasta --prefix /path/to/output/` and...
I want to generate reads with 5000 long and 0.85 accuracy, so I used following command in linux: `pbsim --data-type CLR --depth 20 --model_qc /usr/share/pbsim/models/model_qc_clr --length-min 5000 --length-max 5000 --accuracy-min...
