-
Hi
I am running the assembly using metaspades. Below the final lines from the log, I don't see any error. I am getting an empty file for the final_assembly.fasta. Which file should correspond to thi…
-
Hi,
It seems that octopus open one temporary vcf file per contigs/scaffolds. For many non-model species, there are many contigs/scaffolds in their reference genome, for example https://www.ncbi.nlm…
-
Dear Dengfeng,
I am using purge_dups on a diploid canu assembly (haplotypes not collapsed during assembly because of high heterozygosity). I have run step 1-3 of the pipeline (I don't have an alter…
-
I ran hifiasm (trio) on 3 SMRT cells of diploid CCS data for a F1 hybrid on which I have parental Illumina data. I expect two haplotypes around 2.8gb, however, the size of the haplotypes is drasticall…
-
I have 20 de novo hybrid genome assemblies (ONT plus Illumina; flye plus pylon polishing) of different strains of the same species.
For an initial genome reference, we also have a high quality (T2T,…
-
https://ftp.ncbi.nih.gov/genomes/
https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/
List of `refSeq` sequences: https://ftp.ncbi.nih.gov/genomes/refseq/assembly_summary_refseq.txt
Example: [direc…
-
Hello!
I'm using the Yahs pipeline and creating a sorted scaffold .hic and .assembly file that shows the contig boundaries in Juicebox.
Is it possible to convert my .hic and .assembly file to a…
-
Hello,
I am writing here as I could not find a google group for yahs. This is not a software issue, more of an unexpected behaviour in my data I could use help interpreting.
I am working with Pa…
-
I am scaffolding several ONT+illumina assemblies (flye) against a T2T reference genome of a sister species. Each of my assemblies represents a specific strain of my species of interest--so while I exp…
-
Hi,
I am trying to run masurca_scaffold.sh using two pacbio assemblies generated from some other assembler. I am using main assembly (closest to the estimated genome size) as -r and another assembl…