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Hi,
I am trying to align a .fastq file(16GB) to a genome graph(4GB). Could you please suggest me how many memory and threads should be prepared for successful running?
Thanks!
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@cmarkello has some graphs that have taken over 9 days to GCSA index and are still going.
They were built with the GRCh37 1000 Genomes data, and he's using the GBWT haplotypes to prune the graph befo…
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Hi Jonassibbesen !
In add_haplotype.sh of making pantranscriptome for 1kg_all_af001_imgt_hla_p10k_noB258_noN_a100_gencode100 :
-using this command line : "aws s3 cp s3://vg-k8s/users/jsibbesen/vgr…
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Dear all,
When learning how to detect SVs based on the `pggb` constructed graph genome using `vg giraffe`, I found that the results are a bit strange. And this may be due to the absense of the back…
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Hi Chris,
I have been trying to use HISAT-genotype's transcriptome reference graph, but I can not make it work. It keeps getting killed, and generates an error due to certain files that are missing…
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I tried to generate landscape using the script after divergent calculation, it returns empty HTML include some of the classes not all, what if I wanted specific classes would this be possible? for exa…
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Hello,
I am trying to use purge_dupes on my Nanopore-based genome assembly. Heterozygosity is estimated (using GenomeScope and Illumina data) to be ~3% in this organism, which has a 1C genome size of…
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Hello Developers,
I've successfully built a pan-genome consisting of 12 genomes using MC without any problems. Thank you for your kind descriptions on GitHub.
Now, I'm planning to find more SVs …
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I'm attempting an assembly (relatively heterozygous diploid genome; 5Gb haploid size; with Hifi, ONT & Hi-C).
In the directory 7-consensus, the uniting-popped fast = 7.3Gb; however the uniting.popp…
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Hi, I try to use get_blunted(pre-compile) on graphs which are compacted de Bruijn graph from Bifrost. My system is centos7 with gcc 9.4.
I test all the graphs which construct with 2 or 10 or 100 …