nPhase

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Any advice on how to create a haplotype-resolved assembly form the phase FastQ reads

4

I now have phased nanopore reads from nPhase. Thank you very much for the tool and your help so far. Now, the task is to generate a first haplotype-resolved assembly....

mdondrup

nphase takes a long time at GATK step

4

I am now running nPhase on my real data and noticed it takes a very long time to finish. My data is yeast ONT reads with ~120X coverage and Illumina...

mdondrup

nPhase needs a guide/tutorial for working on large/very heterozygous genomes

2

As long as nPhase doesn't make efficient use of heuristics to drastically speed up prediction time, users will run into issues with trying to run it on large genomes and...

OmarOakheart

Duration and Heterozygosity

28

Hi I'm trying to run nPhase on a tetraploid yeast genome I seqeunced with PacBio HiFi reads. Here is my code: `nphase pipeline --sampleName trialRun1 --reference s288c.fa --longReads pacbioHiFireads.fastq.gz --longReadPlatform...

rmormando

Extract phased variants or reads

5

Hi Omar, Thanks for sharing this great tool. I was wondering if there is a way to export a phased vcf or tag long reads with their haplotype group as...

Adamtaranto

Running nPhase partial with mapped short reads

4

Hi! I have an issue when trying to run nPhase partial (version v1.0.12) using both mapped long reads and mapped short reads. Running: nphase partial --sampleName $ID --reference $ref --output...

jdenkena

nPhase is too slow/memory intensive

1

Right now nPhase is deterministic, meaning it doesn't use any useful time-saving heuristics. It also makes no use of parallelization. Generally it isn't optimized. It would be good to work...

OmarOakheart

nPhase on one chromosome

3

Hi, I am working on tetraploid potato and trying to run nPhase on my dataset, but as you mention yourself it is very time consuming and I had to terminate...

elsasverris

Whenever someone wants to run nPhase on a very heterozygous, large genome and runs into memory issues/takes too long to run, I recommend subsampling the vcf down to a 0.5~1%...

OmarOakheart

ZeroDivisionError in assignLongReadToSNPs when samLines < 100

1

Hi, I've come across an edge case whilst messing around with the tool. When the number of reads in the long-read alignment file is less than 100, the following code...

a-lud