questions about vg autoindex

[Tonitsk8264]

I have the following questions, can you help me answer them?

1. I want to know what the command of each step should be if vg atuoindex --workflow mpmap --workflow rpvg is run step by step. I want to know the steps.

2. To build the index, can it only be built for a single chromosome separately, or can it be built for all chromosomes. If only a single chromosome can be processed, how can the final results be merged?

grateful.

[jeizenga]

The set of equivalent commands varies depending on the input, but they're generally similar to the scripts in these repositories:
https://github.com/jonassibbesen/vgrna-project-paper/tree/main/scripts/bash/contruct_pantranscriptome
https://github.com/jonassibbesen/hprc-rnaseq-analyses-scripts/tree/main/graph_construction/minigraph_cactus_grch38_f1_clip_d9_m1k_D10M_m1k_cat_gencode38_vgrna_k32