minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
I've been benchmarking software that is using mm2 internally. It turns out that there is massive cache miss rate caused by mm2. I ran vanilla mm2.15 on some HG002 CCS...
hi there I got a bam which was created by minimap2 , there is a read with cigar '3S1462M**4D4I**1176M' , four DEL bases was 'GGGA', but mis-interpreted as four INS...
Hello Heng, After you fixed #392 via the latest release (thanks!), I've noticed another edge case that is—I gues—related issue/feature. I am observing some alignments that are showing CIGAR with...
I have just come across this behavior testing out mappy on a genome file that I had accidentally moved. `mappy.Aligner` is able to initialize with a non-existent file, but any...
Hi When I excute mappy with paired ends like aligner.map(seq1,seq2, MD=True): MD string for second reads is wrong. for example for 100nt length perfect match, it reports. 0T2A0G1C0T0C0A0T0T1T1T0T0G0C0C1A1G0C0T0G0G0A0G0T0G0C1G0T0G0G0T0G0T0G0A1C0T0C0G0G0C0T0C0A0C0T0G0C0A1C0C0C0C0C0A0A0C0C0C1C0A0C0T1C0C0C0A0G2T1A0A1C0G0A1T1T0C0C0T0G0C0C I think,...
Hi, Heng! We experimented with Drosophila melanogaster genome and found several strange things in minimap2 behaviour (Version: 2.8-r686-dirty). I've attached two our files for reproducing the issues (full chrX extracted...
Hi, I see the following somewhat weird data (SAM format) coming out of minimap2: ``` L0/46/0_12879 256 L0/46/0_12879 1 0 8963M116I28M116D203M110I9M1I15M1D22M110D3412M * 0 0 * * tp:A:S cm:i:15 s1:i:126 NM:i:454...
Hello, Is there any option to deactivate the Z-drop heuristic when aligning with Minimap2?
Thank you for the amazing tool. Feature request: optional compress index when saving it to disk? My evaluation suggests that running gzip on the .mmi index can compress it by...
Hi, Thank you for your work on Minmap2 and many other tools! I am interested in using minimap2 as part of a pipeline that involves aligning divergent (ANI 75% or...
