DeepSimulator
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liyu95
The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.
When a small (2-20kb) reference contig is used it appears that a significant portion of reads generated are the complete reference genome and have the exact same sequence (IGV trace...
I would like to adjust the repeat time for analyzing the reads. In 'deep simulator 1.0' paper as attached in the pdf, there is a parameter in page number 7...
Hello, I've read the DeepSimulator1.5 paper and there doesn't seem to be an indication on whether it was trained using R9 or R10 chemistry. DeepSimulator seems to have been trained...
Hi, I would like to compare the basecall result (from alignment paf file or pass/fail.fastq file) with the sampled fasta file (sampled_read_processed_genome_*.fasta ) to see how the basecalling goes for...
First I'd like to say thanks for this excellent tool... the application and feature sets fits my needs perfectly. However, to future proof your code you might want to consider...
Hi, I'm trying out DeepSimulator on a Bacterial genome where the input fasta has 3 sequences ( chromosome, plasmid_1, plasmid_2). What parameters do I need to set to get, say,...
Hi, Thanks for providing this tool. As ONT raw accuracy is rapidly improving, I wanted to check if you're able to support base-calling using ONT's latest protocols. Currently, ONT provides...
Hi, Thanks for the great program. I installed it without error but got an error related to TenserFlow when I test it. Can you please help us? > deep_simulator.sh -i...
Hi, Please, I would like to know if the dRNA produced by DeepSimulator would contain RNA modifications. I guess that it would depend if the training datasets for dRNA contained...
When I use example fasta files, it works well. However, when I use my fasta files, it comes to an error like this. dzha@DESKTOP-4U9JHDU:/mnt/d/ape/Deepsimulator$ ./pore_model.sh ../test/random_a.fasta 1 0%| | 0/1...
