minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Hello Dr. Li @lh3 , Do you think optimizing the chaining function mm_chain_dp with the forward computation transformation from will maintain bit-exact results given you calculate st dynamically and Guo...
Hi, I am using minimap2 to map PacBio long reads to genome. Here is the command I ran: ```shell /share/programs/minimap2-2.16_x64-linux/minimap2 --split-prefix prefix -t 9 -a ../01.reference_file/reference.fa ../00.raw_data/m54217_190219_070744.subreads.fasta.gz > m54217_190219_070744.subreads.fasta.gz.sam ```...
Hi. I see this repository uses travis-ci.org. Travis CI announced 2 days ago that Travis-ci.org shut down will occur on May 31, 2021. https://blog.travis-ci.com/2021-05-07-orgshutdown We need to migrate travis-ci.org to...
- added a basic ARM64 test to run through GitHub actions (runs via a docker based on qemu-arm) - added a basic python test to run through github actions (runs...
Hi, I have long (4,500 bp) amplicon sequences of eukaryotic rrna operon, and was wondering would it be possible to annotate them taxonomically using minimap2 against a specific database, say...
I've experienced a memory leak when using the python `mappy.Aligner` when initialized with a sequence file/FASTA (this is within [Megalodon](https://github.com/nanoporetech/megalodon)). This same memory leak does not occur when the `Aligner`...
Thank you for all your excellent work on minimap2, we use it every day. I'm trying to convert the NCBI GRCh38 RefSeq annotation to BED format for aligning with minimap2...
Hi, I'm working on a modified dataset with a noise profile different from standard ONT and used LAST-TRAIN to train scoring parameters to map 90% reads. Directly applying these indel...
Hi, I am using minimap2 to map long ONT reads (up to 400Kbp), and I am finding that the supplementary chaining is producing large rearrangements in the read sequence, flipping...
