Hasindu Gamaarachchi

- added a basic ARM64 test to run through GitHub actions (runs via a docker based on qemu-arm) - added a basic python test to run through github actions (runs...

Option to set a cutoff read depth when calling variants for regions with exotic depth

1

I am running nanopolish variant calling on chr22 of a NA12878 dataset. I generated small regions using the *make range script* and launched multiple nanopolish instances using *parallel* command. However,...

cleaned up GPU consensus calling

10

This pull request restructures and cleans up the pull request #468 (GPU accelerated nanopolish consensus) by @vellamike so that: 1. it can be automatically merged; and, 2. changes to original...

Methylation aware polishing has been now implemented for the GPU. The answers from CPU and GPU for multi-model (-q dam,dcm) now match The vcf resulted from CPU and GPU for...

Extracting a subset of data from raw nanopore signal data

5

I was looking for an ONT raw signal dataset at very high coverage (a few 100X) and the nanopore dataset in this repository seems to be ideal. It is just...

Segmentation fault during polishing step

4

Hi, I have been recently attempting to polish a draft (human genome) constructed from a PromethION sample. However, at the polishing step, it returns a segmentation fault. Any suggestions on...

Models for newer versions of Guppy with sup basecalls

3

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....

POC only. Rest is left for your self haha

Hi Jared, I got a couple of issues with this polyA program in nanopolish giving `READ_FAILED_LOAD` (e.g., https://github.com/hasindu2008/f5c/issues/152) which we fixed a little after the v0.14.0. However, most users download...

Hi, Can I know how this `.rawsig` can be generated from a dataset that I have? Is it the pico-ampere converted signal or is it also normalised? Sorry if I...