minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Hi, I noticed that if the primary alignment is chimeric (multiple tp:A:P tags) and say one or multiple pieces of the alignment has a low alignment score (ms or AS...
Hi Heng and team, I recently used minimap2 on a set of reference sequences whose sequence similarity might be high. I got abnormal percentage of singletons (`-326.79% are singletons` as...
Hi, I am using the following command to align the raw scRNA-seq data from PacBio: ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam I checked the aligned file and there...
Dear Heng and team, Recently I ran minimap2 to align HG002 (alt) to GRCh37 (ref) with default settings to facilitate SV detection. The alignment result showed biased distribution of short...
Dear Heng and team, we are aligning polished IsoSeq reads against genomes and I noticed a few cases where the last exon of 13 bp was softclipped and not aligned....
Hello I would like to understand why the reads are not(less) mapped in proper pairs when --split-prefix is used ? **with split-prefix (index .mmI < target size)** (25% in proper...
Hello, When doing a whole genome liftover, the resulting bed files contain flags of _t3 or _t5 on some of the lines as seen: chr1 78142605 78143033 chr1_78599500_78600455_t5 0 +...
HI, @hyphaltip @jmarshall @junaruga @jts I want to know, how to use the minimap2 to map the HiFi reads to ONT reads? Thanks!
Hello, Thanks a lot for minimap2, it'a great tool that I use almost every day ! I'm working with ONT sequences. I know that there is a -x map-ont preset...
Dear Dr. Li, I am currently trying to achieve shortest runtime by utilizing the available resources on the HPC that we have at the moment (128 threads CPU with 128GB...
