minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Hi! I have been using minimap2 as a part of the Flye pipeline. I am using secondary alignments during consensus/polishing to account for possible duplications in disjointigs and improve the...
Hi @lh3, I'm benchmarking my aligner against minimap2 and got a reviewer comment about evaluating performance with (eventual) future Illumina chemistry X reads. I am therefore including longer simulated Illumina...
Hi, I would like to understand the difference between the FLAG "256" and "272" in SAM files. I understood that they are both involved in "secondary alignments" (https://github.com/lh3/minimap2/issues/4). However, I...
use -c for cigar, the error : minimap2: align.c:125: mm_fix_cigar: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed.
Hi, I am trying to run minimap2 as part of purge_haplotigs, but minimap2 gives me an error which I think is caused by minimap2 and not by purge_haplotigs: ``` $...
Hi, I would like to know more about the --split-prefix option. I have a very large (1200 GB) index that I want to align and I of course don't want...
Hello, using the version 2.20-r1064-dirty; ``` minimap2 -t 8 -d ventricosus.mmi long_contigs.fa minimap2 -X -t 8 -K 50M ventricosus.mmi long_contigs.fa > ventricosus.self.paf ``` returns ``` [morecore] insufficient memory [1] 139113...
The program [align.py](https://github.com/lh3/minimap2/files/7816510/align.py.txt) uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to...
Hi Heng, I am looking at a 1 Mbp region on chr16 that doesn't seem to align when comparing GRCh38 and T2T, but there is a lot of homology in...
1. Will map-hifi preset work for Nanopore super accuracy model? 2. Will you have preset option for Guppy v5.0.7 (super accuracy model) soon?
