NanoSim
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bcgsc
Nanopore sequence read simulator
Hello, I am using the chimeric read simulation function, and would like to use the position of chimeric region introduced by the simulator. However, I can't make sense of the...
Hi, Thank you for a great tool. I had a couple of questions. 1) The cell line NA12878 is heterozygous at about 2M or so sites. When generating the simulated...
Hi, I've characterized and later simulated 20000 reads from the E. Coli genome. It seems that the simulated_aligned_reads.fastq file generated in the simulation phase isn't a valid fastq file, according...
I've just cloned the most recent version and ran it with pre-computed and newly computed profiles. Got no errors or warnings, but weirdly, all reads I obtained were perfect, i.e....
simulator.py genome FileNotFoundError: [Errno 2] No such file or directory: 'training_model_profile'
https://github.com/bcgsc/NanoSim/issues/11#issue-204760214 This bug happened again: (nanosim_env) lishuxian@tong1:/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file$ cat list.fasta.txt | while read line; do /mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py genome --fastq -rg filtered_${line}.fasta -b guppy -n 100000 -t 40 -s 1 ; done running...
HI NanoSim developers, I am wondering if you have a pre-trained model for simulating genomic reads from the human genomes close to ones basecalled from newer versions of Guppy (e.g....
Hi, Thanks for the software to simulate nanopore reads. I get a bit confused while using the simulator.py with --number. From the help message, --number suggests the number of reads...
My commdand-lines: ``` # NanoSim v3.1.0 singularity run -B /nfs/ nanosim_v3.1.0.sif read_analysis.py genome \ -i all.pass.filt.fastq \ -rg 741_wzi_types.fa \ -o training \ --chimeric \ -t 40 singularity run -B...
Any plan to add `dorado` to `--basecaller`? Thanks.
Hi - I'm trying to simulate data similar to that generated by the [nCATS](https://pubmed.ncbi.nlm.nih.gov/32042167/) protocol. What this means is that I would like to be able to specify e.g. one...
