nanopolish

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Can fastq be indexed without indexing fast5?

4

I am using nanopolish to call methylation. As far as I can tell `nanopolish index` indexes the entire contents of a fast5 folder and a single fastq file. So for...

Shians

Please port to Python3

11

Hello, the Debian Med team is maintaining nanopolish for official Debian. The recently released Debian 10 was the last Debian release featuring Python2 since this programming language is EOL. If...

tillea

This branch provides functionality to score variant candidates using a GPU. Measured acceleration of overall polishing application is between 2x-10x and depends on score threshold and coverage.

vellamike

quickstart - calling methylation with nanopolish issues

1

hi, a couple of things i noticed when running through the tutorial mentioned in the title: The compare_methylation.py is slightly broken. I followed the quickstart guide and when i got...

daanverhagen

Detection of 2′-hydroxyl modifications in direct RNA-seq data

3

Hello Jared, I'm new to Nanopolish but would like to use your software for detection of RNA's native structure, similar to SHAPE-map presented during London Calling 2019. Recently, generated two...

s-t-calus

concordance in variant calling using down-sampled bam files

5

I called variant from the main bam file, then I did the same thin using after down-sampling the main file using samtools `(-s 0.1, -s 0.2, -s 0.3, up tp...

herrroaa

call-methylation returns non-CG methylated site?

4

I ran the example in https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html. However, I noticed that some reported coordinates were not pointed to C/G base and probably shift -1 base. For example, in `methylation_frequency.tsv` ``` chr20...

cgjosephlee

To remove the outliers from the raw signal. 

awjga

Using eventalign to align raw RNA signal with high error

2

Hi Jared, I am using eventalign to align signals from direct RNA sequencing. However, as the RNA that I am sequencing is expected to have a signal that is different...

awjga

RNA event alignment shows T's rather than U's in model kmer

2

Hello. Thank you for your great work. I’ve found nanopolish to be an excellent research tool. My question relates to the “Model kmer” field in the event_align output; I am...

Blosberg