minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Hi, I am attempting to use your example.c as a template for aligning some assembly haplotypes: https://github.com/rlorigro/GFAse/blob/0ce1fb2990bce9b0f4ab27dade77ff1263402deb/src/test/test_minimap2.cpp#L39 Target: https://github.com/rlorigro/GFAse/raw/main/data/long_challenge_node.fasta Query: https://github.com/rlorigro/GFAse/raw/main/data/short_challenge_nodes.fasta My adaptation of example.c tries to apply the the...
In the Limitations section you write. - Minimap2 often misses small exons. Can you define "small exons"? what's the range? there are exons of 3 bps just to be clear.
Thank you all for providing the paftools.js call utility! The output file for the call command lists start and stop coordinates. I belive the start is 0-based (like a bed...
I used minimap2 for mapping ONT reads with the plant mitochondrial genome database and obtained sam file. I would like to know how to extract potential ONT reads in a...
### Steps to reproduce: 1. input sample: [sample.fa.gz](https://github.com/lh3/minimap2/files/9056559/sample.fa.gz) 2. reference genome: wget https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.gz gzip -d hg38.fa.gz 3. download minimap2: curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf - 4. Run ./minimap2-2.24_x64-linux/minimap2 -t...
Hi, I am using minimap2-2.24_x64-linux for mapping genome assemblies. After mapping them with minimap2 I would like to convert the sam output to a bam output, when I try this,...
This patch freads multiple pairs from the index file rather in single pairs for efficiency. On my tests, this reduced run time during index load of a short read index...
when I used the nanopore data to map the Illunima raw data (150bp), the minimap2 was warnning as blow: [WARNING] For a multi-part index, no @SQ lines will be outputted....
This patch changes Makefile.simde such that it compiles on aarch64 Linux using SIMDe. GCC will error on aarch64 with the "-msse4.1" flag - so this is removed for aarch64. However...
Dear heng, thanks for the fantastic tool. I have some questions, can I use minimap2 to align pair-end 150bp short reads to assembled contig of these short reads, how is...
