ngmlr
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philres
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
I'm using the following version of ngmlr: `ngmlr 0.2.7 (build: Jul 3 2020 03:31:03, start: 2020-07-19.14:10:32)` I ran the following command: `ngmlr -t 8 -x ont -r $reference -q $file.fastq.gz...
Hi Devs, The IGV screen shot below shows the same deletion in short reads above (BWA-MEM) and ONT reads below (NGMLR). The 22bp deletion is strewn across ~50bp of the...
Hi, May I know the formula of mapping quality in sam. I wonder how to calculate this value, and the threshold of high mapping quality. Thanks.
HI - I have read through your docs/paper and previous issues but have not found a detailed description of how soft clipping and read splitting work. Could you please point...
Hello, I'm analysing some Cryptococcus neoformans (a haploid fungus) PacBio genome data. I noticed something strange when I was looking at some deletions which had low allele frequency. When only...
Dear all, First of all, thanks for this very nice development. I just wanted to report the fact that on some quite heavy ONT runs from bovine, NGMLR followed by...
Did high coverage PacBio sequencing of a human donor (about 8.5 million reads). Trying to use NGMLR to map to GRCh38.p13 Running on a system with an i9-9900K (8 core)...
we found this panic at some OS： ``` ngmlr[315]: segfault at 564a2f0316a5 ip 0000564a39f5440a sp 00007febb91f8450 error 4 in ngmlr[564a39f38000+3d000] ``` then use gdb found： ``` Program terminated with signal...
I am running NGMLR with a polyploid using raw PacBio reads. It always crashes with the following output. I have tried to check the validity of fastq using tools like...
