John Davey

+1, just saw this with a set of 2,408 OrthoDB sequences against some MinION data: ``` $ mash sketch -a -i gene.orthodb.fasta $ mash screen -p 30 -w gene.orthodb.fasta.msh reads.fastq.gz...

Thanks for the quick response. This works for the GTF, so I can continue with that, but just to let you know, it doesn't work with the GFF (maybe a...

Thanks - I'm polishing with 600x coverage of the genome in MinION 9.4.1 reads called with guppy 3.1.5 from a Circulomics library - >50x coverage in >50kb reads. I'll try...

Ah! That might explain it to some extent. We have noticed that nanopore only sequences telomeres in one direction - reads are present with telomeres at their ends, but no...

The numbers are total telomere count, for a 6bp telomere - so for example the tig00000084 contig has lengths something like this: ``` Telomere count 61 25 1 0 0...

Thank you very much for this. I've tested the branch with and without the `--no-trimming` option. I subsampled the sequence, alignments and reads for tig00000084, using the original PAF file...

The contigs definitely share overlaps at the ends, because they are full chromosomes, and they all feature roughly similar subtelomere sequences ~10kb long. This definitely caused small reads to pile...

Hi @cgjosephlee - thank you very much for this, I can confirm that using minimap2 -c for racon alignments retains the telomeres! @rvaser, please could you consider mentioning this in...

Are they completely removed, or just trimmed? Is it progressive? I saw some of my telomeres altered in length, which I took to be appropriate refinement of the true telomeres,...

Hi @cgjosephlee - can you retain telomeres using minimap2 -c (PAF + Edlib alignments), rather than minimap2 -a (SAM + ksw2 alignments) & --no-trimming? It's great that the latter works...