nanopolish
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jts
Signal-level algorithms for MinION data
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...
Hi, The conda binary ignores the thread option for `eventalign` mode (at least). I could verify that the git-make-based installation runs with the palatalization on the same system. So there...
Hi, yesterday we've run `nanopolish call-methylation` according to [Live methylation calling](https://simpsonlab.github.io/2020/03/03/nanopolish-v0.12.0/) instruction. ```shell NCALLS=12 time parallel -u 'nanopolish call-methylation -v \ --progress \ -g "'"$REF"'" \ -t "'"$THREADS"'" \ --watch-write-bam...
When the user provides a sequencing summary file for a partially basecalled run, many reads will be indexed the slow way without indication to the user. Provide better messages in...
I recently ran quite a few DRS libraries and want run poly-a analysis using nanopolish. I'd say its only worth running on PASS reads. However, I am running into the...
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...
FYI - vanilla 0.12.0 + recent commits (HEAD) ``` g++ -o src/nanopolish_methyltrain.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -I./include -I./htslib -I./minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model...
Dear Jared, For one variant Nanopolish is calling a Hom position as het. Below the INFO `155205331 | . | T | C | 1794 | PASS | BaseCalledReadsWithVariant=188;BaseCalledFraction=0.817391;TotalReads=222;AlleleCount=1;SupportFraction=0.900699 |...
Dear Jared, Thank you again for the great software. I am having some issues with one variant not being called correctly from Nanopolish. In that position, the reference has a...
From @hasindu2008 1. `model_name` field in summary output is missing 2. window region command line argument is inconsistent with other subprograms