minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Hello I am trying to use minimap to align genome assembly to a reference genome. Since the genome is very large, (~10GB) I have split the new genome assembly to...
Hi everybody, I have used MiniMap2 to map an assembled genome (generated with oxford nanopore reads) on a public reference, I did it to find the regions in common and...
Hi everyone. I am using `paftools.js call` to call the variants from an assembly to reference mapping. I used the following lines: `minimap2 -cx asm10 --cs reference.fa assembly.fa | sort...
Hello everyone, I have used minimap2 to map nanopore reads to a genome assembly I want to improve. I used the following command: `minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam...
Hi, Thank you for tool @lh3 ! I have a question： My target sequences is a little big (56 G), When I ran a alignment， 9000 reads running for 15...
Hello, I want to alignment a query sequence with up to 30% sequence divergence or higher (may be up to 40% sequence divergence). Could you please tell me how to...
Hi, I used minimap2 (2.17-r941). The `NbV1ChF.fasta` and `ragoo.fasta` are 2.8 G and 3.4 G. However, I ran out of memory on 2 TB machine. ``` minimap2 -ax asm5 --cs...
Hi Heng, We have an allotetraploid genome and I wonder that we can separate fragmented contigs into the exact group in allotetraploid genome. Simply can we keep only best hit...
Hi, I use minimap2(2.17-r974-dirty or 2.17-r941) to map pacbio data to fasta. It works well at the beginning, and then got this error as below: `[M::worker_pipeline::8353.332*54.76] mapped 18539 sequences /var/spool/slurmd/job20248750/slurm_script:...
Hi, Mapping a small set of reads (6) against two identical references (but with different names), gives different results when the order of the reads is reversed. The dataset: [Archive.zip](https://github.com/lh3/minimap2/files/5595692/Archive.zip)...
