DayTimeMouse

Hi, Thanks for developing this tool. I have mentioned this issue https://github.com/Nextomics/NextPolish/issues/136. I have already used no Ns scffolds.fa, and record Ns' positions and counts. However, polished assembly size is...

The variants are almost Silent

1

Hi, When I use read.maf to read maf file, but almost variants are silent(silent variants/all variants: **16874**/17013). I am unsure about that is annotation problem or something. `df = read.maf('filter.vep.maf')`...

Hi [chhylp123](https://github.com/chhylp123), In order to generate gap free haplotype genomes, I want to use p_ctg.fa and a_ctg.fa(Or assembly genome by another assembler) to fill the gaps of hap1.fa and hap2.fa(Like...

Hi, Thanks for developing this nice tool. I have my own FASTA and GFF files. How can I use these files to annotate a VCF file and convert it to...

call somatic SVs

1

Hi, Thanks for developing this awesome tool. I'd like to call somatic structural variants (SVs) using paired tumor and normal samples. However, cuteSV can only process one sample at a...

evaluation for QV in haplotypes

3

Hi, Thank you for developing this nice tool. I have obtained hap1.fa and hap2.fa using hifiasm(HiFi +HiC reads). Next, I would like to evaluate the QV and completeness of each...

Coordinate Conversion Before/After Variant Calling?

2

Hi, Thanks for developing this nice tool. I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of...