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
Hi, I run the ngmlr followed command --`ngmlr -t 10 -r $ref -q $reads --rg-id Pse2Mcin --rg-sm Pse -o out.sam`. After running done, I use the samtools--v1.9 to convert sam...
This issue is somewhat related to #75 I use NGMLR to align data produced by nanopore using the command: `ngmlr -t8 -r ./reference.fa -q ./reads.fastq -o ./output.sam -x ont -bam-fix`...
Good morning, I'm having an issue with alignment and subsequent sorting of files. My pipeline is: sequencing with MinION (Nanopore), basecalling and demultiplexing with Guppy, alignment with NGMLR, sorting with...
Hi, I noticed that the preset for ONT (`-x ont`) is commented out in the code: https://github.com/philres/ngmlr/blob/8d7677929001d1d13c6b4593c409a52044180dca/src/ArgParser.cpp#L258-L266 This makes the behavior for `-x ont` identical to `-x pacbio`, the default...
Hello, I run "ngmlr -x pacbio -r ref.fa -q query.fasta -o query.sam", and got error "Segmentation fault (core dumped)". I have been split the fasta file into many part, also...
Hi all, I cannot find the documentation to explain some of the SAM flags (see an example below). Can someone help explain? `AS:i:715 NM:i:11 XI:f:0.9722 XS:i:0 XE:i:715 XR:i:393 MD:Z:142T82T45^C9A8^A3^A17G21G8A50 SV:i:2...
You could incorporate nvidia cuda code to increase execution speed ... It's just a suggestion
Any suggestion to improve the run time of ngmlr jobs. An average job run time is 35-40h, I have tried to increase the number of threads also, tried to use...
Hi, The last release was in June 25, 2018 Since then since some fixes have been merged and it has been ~3 years since then, could you please tag a...
I am trying to run PacBio data against a mouse genome, and am seeing the following error `Error in 'ngmlr': double free or corruption (!prev): 0x00002aaed8eeb910`. I am running the...
