Hung-Wei

Input file and genetic map requirement

2

Dear all, I am a beginner of using this powerful software. After reading the manual and other related issue, I would like to confirm about the input file format and...

Can I use MITObim with Nanopore reads?

2

Dear community, According to the manual of MITObim, this useful software can use PacBio long reads for mitochondria assembly. Can I use Nanopore long reads, too? Thank you.

Dear @hardingnj and community, I would like to ask whether it's better to use the artificial F1 vcf file to run XP-CLR for selfing species. For some crop species, they...

Dear community, As I know, the organelle_PBA is designed for organelle assembly with PacBio long-read data. I am curious whether I can also use Nanopore long-read data in organelle_PBA? Thank...

Question about order of population set when running Dtrios

1

Dear @millanek and community, I have questions about the order of population set when running Dusite Dtrios. If I have 3 populations (P1, P2, P3) and an outgroup population, the...

Question about plotting RCCR result and -s option in cross population analysis

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Dear @stschiff, 1. According to the general guide (https://github.com/stschiff/msmc-tools/blob/master/msmc-tutorial/guide.md), the partial script to plot the RCCR result is: > xlim=c(1000,500000),ylim=c(0,1), type="n", xlab="Years ago", ylab="relative cross-coalescence rate" I would like to...

Identify the homology of tetraploid genome

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Dear @chhylp123 and developers, Thank you for the useful and convenient software for genome assembly.Recently, we assembled a tetraploid plant genome (2n=4x=40; It may be allotetraploid). I would like to...

suggestions of the script to identify the homology in tetraploid species

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Dear @zhangrengang, Recently I want to identify the homology of the de novo assembled genome from the tetraploid plant species for running SubPhaser. As you suggested before (https://github.com/zhangrengang/SubPhaser/issues/4#issuecomment-2564572679), currently I...

Unexpected “X” characters in FASTA output from vcf2phylip

1

Dear @edgardomortiz , Thank you for providing this convenient script for generating alignment sequence files. When I ran vcf2phylip (v2.9) with my VCF file: ``` vcf2phylip.py -i 20250812_filter.vcf.gz --output-prefix 20250812_filter_alignment...

Hi, I have a question regarding bcftools filtering behavior. I’m currently testing test.vcf (10 samples, 20 bi-allelic SNP sites) and would like to verify whether my filtering conditions work as...