Question abou GNU Parallel to run 3D-DNA?

[mushroom astar]

Hello!

With your help, I have successfully run juicer 1.5  and generated files merged_sort.txt.

l want to ask two questions.

First, l use the hifiasm to complete genome assembly and use the "hic.p_ctg.gfa"  diploid  version of the genome and when using 3D-DNA which  "-m|--mode haploid/diploid" should l use?

Second, l find that you recommend  "GNU Parallel >=20150322 – highly recommended to increase performance" but l am not sure how to use this by me.

Now l have installed parallel"GNU Parallel 20210722" and l would like to ask how to do use this to speed do our step.

My code is as follows"                                                                                           

run-asm-pipeline.sh test.fasta merged_nodups.txt

Waiting for your reply!

Thank you!

[Olga Dudchenko]

Hi TanXing,

Sorry for the delay in answering.

We no longer provide support for diploid version. The default mode of operation is haploid, and if you see signal associated with undercollapsed heterozygosity the recommendation is to purge, using either standalone software or parameters in hifiasm. p_ctg is primary, mostly haploid, there is no problem with using that.

You do not need to do anythign special to use GNU parallel: as long as it is in the path 3d-dna will find it and use it. If it is not in the path for your user 3d-dna will complain.

Best,

Olga

[mushroom astar]

OK~

Thank you very much for your reply. I have now completed this step and it runs quicker than before.

mushroom astar