minimap2
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A versatile pairwise aligner for genomic and spliced nucleotide sequences
I have bunch of Oxford long-read fastq files that I need to convert to sorted bam files and later assembly using stringtie. I ran the following command for conversion from...
Hi, I have received the following error message when running minimap2 step in ```purge_haplotigs```. ``` [M::main::12.417*0.75] loaded/built the index for 7855 target sequence(s) [M::mm_mapopt_update::14.333*0.78] mid_occ = 412 [M::mm_idx_stat] kmer size:...
I used below command to map one wheat genome against reference in a 32 cpu and 1TByte machine. minimap2 -x asm5 -f100 -K4g --cs=long -t 32 --secondary=no iwgsc_refseqv2.1_assembly.fa arinalr_sm.fa |...
Hello Dr. Li, We are running minimap2 as part of a viral haplotype detection workflow and have noticed some weirdness between different reference files. `all_viruses.fasta` contains viral variants (many accessions)...
Hello, I have a very specific proble regarding the mapping of some special ONT reads. These reads are sometimes made of a part with an high mutation density and another...
Hi Heng, This isn't necessarily a bug, but I was a bit surprised. Also, this definitely is not a high-impact issue. So, this is arguably an edge case. When one...
Hello, There is no explanation of the zd flag in paf format in the minimap2 man page. This one is in the same field as the rl field. Do we...
Ensure compiling on aarch64 is seamless by default by autodetecting aarch64 using POSIX standard `uname -m`
Hello, I am currently using minimap2 v2.26 and I have a question regarding aligning two fastq files. I have used the following commands: `minimap2 -cx map-ont A.fastq B.fastq --secondary=no >...
Using mm2 v2.26 in `pbmm2`, I fail at ``` lchain.c:228:1: runtime error: index -1 out of bounds for type 'const lc_elem_t *[64]' (aka 'const struct lc_elem_s *[64]') ``` How to...
