Manish Goel

It would be really helpful if there is a guide on how to generate repeat library for non-humans. @agolicz did you manage to run xTea on plants? Could you please...

I want to use this with syri for genomic differences identification. The size of the sequences can vary (from A. thaliana (130 MB) to humans to oats (10GB)), so it...

Hi Heng, Thanks for looking into it. Continuing https://github.com/lh3/minimap2/issues/823 The current [HEAD](https://github.com/lh3/minimap2/files/7324395/minimap2.v222.HEADout.txt) still requires some more improvements. The 10kbp inversion is still not identified while the 5kbp inversion is only...

Here it is: [ref.txt](https://github.com/lh3/minimap2/files/7324448/ref.txt) [seq_inv5000.fa.txt](https://github.com/lh3/minimap2/files/7324460/seq_inv5000.fa.txt) [seq_inv10000.fa.txt](https://github.com/lh3/minimap2/files/7324461/seq_inv10000.fa.txt) My command: /software/TMP/minimap2_HEAD/minimap2 -cx asm5 ref.txt seq_inv10000.fa.txt

Thanks for fixing this. I tested on some more simulated inversion and it worked fine. The 5k issue didn't happen in any other case, so cant share more examples. Another...

Thanks for sharing the parameters. I understand the limitations in finding small genomic rearrangements.

Are there plans to include this change in the mappy code?

Hi Luca, The test data finished without errors. I re-sorted and re-indexed the `smoothed.selective.bam` file, but the `SVDSS search` command is still not finding any SFS and output the log...

Hi Luca, Here is the output from the smoothing and searching step: ``` (mgpy3.8) 18:18 goel@dell-node-12 netscratch:svdss$ SVDSS smooth --bam sample.bam --workdir . --reference GRCh38_latest_genomic.fna.gz --threads 60 Ping-pong, comparative genome...

It is been quite long so I cannot recall what exactly I had to do, but I think it involved installing some older versions of HD5.