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Thank you for developing such an excellent tool. The paper “Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution” mentio…
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I'm querying my .gff files to pull out sequences for certain genes but it is giving me output in amino acids. I saw in a supplementary document that you can get this outputted in nucleotides but the d…
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I am trying to run query_pan_genome
roughly like this:
query_pan_genome -g clustered_proteins -o output.txt -a difference -i 1.gff,2.gff -t 3.gff
I also tried replacing the -i and -t with --inpu…
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when I run this:
singularity exec $pggb_path/pggb_latest.sif wfmash -t 20 $genome_path/ganganF73.genome.fa.gz --query-file-list=/home/user/huyang/shuai/data/pan_test/genome/genome.txt > aln.paf
I …
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Hi!
I used vg chunk to extract subgraphs from a pan-genome graph and then used vg deconstruct to obtain VCF files for both the pan-genome graph and the subgraph. However, I noticed that the VCF fi…
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In the future, I want to map the resequencing data of different species of onto my map genome.Then the group vcf with good classification is used to carry out the process of vgmpmap
I wonder if this …
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Hello,
Much appreciated for your excellent work.
I try to run your code in my project with pangenome command.
I met a error as following:
Starting ====== 2020-02-27 12:40:48 ======
Traceback…
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The vg version I use: version :
v1.59.0
I used PGGB to construct a pan-genome (GFA); I want to rely on him to find the SNP of the sample; Here's my current script:
vg autoindex -t …
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## The need
Let the user use their own gene clusters for anvi-pan-genome.
## The solution
A flag for anvi-pan-genome to tell the program to not run diamond/MCL, but use a user-defined list of…
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The author made an excellent software. After I tried the genome I was interested in, the accuracy of the software for centromere prediction was indeed much higher than that of the software I used befo…