minimap2
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lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Adds a `cs_long` flag to mappy.Aligner.map, to let Python code get the "long CS" format string. ``` # generate a short cs string aligner.map(seq, cs=True) # generate a long cs...
I have a flagstat file here that looks like this: ``` flagstat 21384 + 0 in total (QC-passed reads + QC-failed reads) 14485 + 0 primary 6899 + 0 supplementary...
Hi @lh3, I'm using slices of NCBI's NT database for pacbio hifi read mapping. I noticed that the number of minimizers seems to have overflowed the integer count. Would you...
@lh3, I was benchmarking the `radix_sort_128x()` function from minimap2 to perform anchor sorting (map.c [[Line 202](https://github.com/lh3/minimap2/blob/0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b/map.c#L202), [Line 289](https://github.com/lh3/minimap2/blob/0cc3cdca27f050fb80a19c90d25ecc6ab0b0907b/map.c#L289)]). For small input sizes of anchors i.e. $\approx 10^5$, `radix_sort_128x()` produces stable...
I have a very long read (~500kb) which I try to align using `mappy` in python using the `MD=True` flag and this gives a Segfault. This read does not align...
We use this patch for the Debian package of minimap2.
We use this patch for the Debian package of minimap2.
As documented in #724, the CIGAR strings used to describe supplemental alignments in the `SA` tags produced by minimap2 are approximate—for example, a CIGAR string of **`23M 1I 537M 1I...
Hello, I am using minimap2 to align several sequences to a transcriptomic reference of about 4000 sequences. There is one reference sequence (let's call it X) to which no reads...
Hi Minimap team, I am using Minimap to align genomes against reference sequence with options: `minimap2 --eqx -c -x `. It seems that minimap misses aligning the first codon if...
