NanoSim

NanoSim copied to clipboard

NanoSim for tuning Minimap2 parameters?

2

Hi there, Thank you for creating and maintaining NanoSim, great tool. Could nanosim be used to fine tune the parameters of Minimap2? If so do you have any recommendation on...

ammaraziz

- Added a new mode "rbk" (rapid barcode kit) to replicate the read distribution seen in Nanopore amplicon rbk data, where forward reads are enriched at the amplicon 3' end...

GeorgetteTanner

Stuck at simulation stage

4

Hi, I am trying to use NanoSim 3.0.0. (downloaded source code from (https://github.com/bcgsc/NanoSim/releases/tag/v3.0.0)) for simulating ONT reads. I created my own profile using: `./read_analysis.py transcriptome -i ont_run.fq -rg ucsc_hg38.fasta -rt...

kainth-amoldeep

ValueError: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 1 is required.

6

I'm getting this issue while running the chimeric and quantification arguments for metagenome mode **ValueError: Found array with 0 sample(s) (shape=(0, 1)) while a minimum of 1 is required.**

Dr-bioinfo

Nanosim hangs in the middle

18

OK, So, We are using a pretrained model for metagenome simulations, We have a standard read count and 2 samples are getting generated, however when we are changing the no....

aastha-batta

Option to specify desired read coverage or sequencing depth

2

Hi there, I am wondering whether there is any option for specifying desired read coverage and sequencing depth for simulation. I only saw the option to specify the exact number...

HLHsieh

Infinite loop in function extract_reads in metagenome mode when length equals max length

2

In the function `extract_reads` when `dna_type == "metagenome"` the while loops checks that: ```python3 length > max(seq_len[s].values()) ``` and: ```python3 length < seq_len[s][key] ``` but there is no case for:...

danpal96

Hi Nanopore comunnity has already published the R10.3 and R10.4 flow cell, with much higher accuracy. I'm wondering is there any models that can be used in R10 flow cell...

zhenLiuXplr

Reads come mostly from one chromosome only

1

Hello - I'm simulating reads from *Leishmania major* genome using training reads sequenced from this genome: ``` read_analysis.py genome -o training -i fastq_runid_ae10a0b01321b03612390f5e1e5fe2b0d834516a_0_0.fastq.gz \ -rg TriTrypDB-45_LmajorFriedlin_Genome.fasta -t 16 simulator.py genome...

dariober

hangs at start of simulation

5

Hi, I'm finding myself stuck at the start of simulations. Im running the metagenome sim. for example it will say : 2022-12-28 23:26:25: Read in seq1 2022-12-28 23:26:25: Read in...

omarkr8