minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
When we assemble a new genome (for example with HiFiASM) we get five useful sequence files: hap1.p_ctg.gfa hap2.p_ctg.gfa p_ctg.gfa p_utg.gfa r_utg.gfa Each captures elements of the (diploid) genome. A future...
I noticed that there are mm, gn, and go tags in the SAM/BAM file converted into PAF using pfatools. However, I couldn't find the definitions of these tags in the...
Hi, I was wondering how -ub, from the splice preset (-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes) may help to map...
Givem a PAF file of one genome aligned to a reference, I can get overall coverage percentages with `paftools asmstat`, but what I would like is a BED file of...
Hello, following this issue: https://github.com/wheaton5/souporcell/issues/179 minimap is used in souporcell pipeline like: https://github.com/wheaton5/souporcell/blob/master/souporcell_pipeline.py#L255#L257 I am out of ideas and thus reach out in case you have any suggestions. I could...
Dear Hang Li and all, After successfully using minimap2 on many occasions, I recently encountered an issue when using an assembly file, produced by hifiasm (v.0.18). Attempting to map HiFi...
TSan complains that this read of |ktf_worker_t::i| is unsynchronised wrt the stores on the other worker threads. Unlike the __atomic_* family of functions the __sync_* functions don't have a relaxed...
I tested 2.17 to 2.24 using an inversion between two large homologous domains. 2.17 and 2.18 detection was possible using structural variant callers. Everything after that was unable to be...
Hey @lh3 We are starting to add alignment support to [dorado](https://github.com/nanoporetech/dorado) and I would like to get some patches upstreamed if possible. The following pull requests https://github.com/lh3/minimap2/pull/1028 https://github.com/lh3/minimap2/pull/1029 fix the...
Hey there, I am trying to align >14Gb allopolyploid wheat genome assembly contigs (N50>30Mb, longest>270Mb) to a >14Gb reference (longest chromosome>850Mb) with the following parameters: minimap2 -x asm5 -t 16...
