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Hello,
I have used Parsnp to generate a core genome alignment for approximately 700 genomes. However, I have encountered several warnings indicating the presence of identical genomes. While these g…
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We discussed this briefly in person on Monday 14 October, but to put this in writing:
The details differ but most if not all of the ANI methods have some threshold below which they find no meaningf…
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Hello,
I have encountered a weird issue when using minimap2 to do whole genome alignment. My data conatins a short assembly A (haplotype) and a long assembly B (diploid). When I used the assembly A a…
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Hi Dr. Song,
When I was aligning the genomes of B73 and mo17 in maize, in the region around 24 Mb on chromosome 4 that I was concerned about, large segments failed to be aligned. The intergenic reg…
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Is it the number of _alignments_ or the number of _reads_ (there can be a 1:many relationship between a read and its alignments)?
> non-primary alignments - number of secondary reads (flag 0x100 (256…
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I am currently conducting Whole Genome Bisulfite Sequencing (WGBS) data analysis using Bismark and plan to utilize a soft-masked genome, where all repetitive and low-complexity regions are marked with…
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I think your objective is clear, but I have some confusion about the execution.
You mention that you intend on visualizing your alignments with `progressiveMauve`. Despite the problems associated w…
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[2024-10-28 04:01:14] INFO: GTDB-Tk v2.4.0
[2024-10-28 04:01:14] INFO: gtdbtk classify_wf --genome_dir new_genome_data/ --skip_ani_screen --out_dir classify_wf_out --cpus 16
[2024-10-28 04:01:14] IN…
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Dear Devon,
Thank you so much for developing this great tool! My colleague recommended bwa-meth and MethylDackel to me.
Recently we developed a haplotype-resolved diploid human genome, where one…
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https://github.com/legumeinfo/LIS-autocontent/commit/a083d8ff07eff2e37e39ed767a51be0616046804#diff-794aa24529bb6da3cad71d57ea1c597df5d654779414fef62732f9bc4f1a1281L186 seems to have deleted the line t…