### Spliced pangenome graphs, pantranscriptomes and indexes

This folder contains graphs, pantranscriptomes and associated indexes. The files are used by vg mpmap (https://github.com/vgteam/vg) for RNA-seq mapping and rpvg (https://github.com/jonassibbesen/rpvg) for haplotype-specific transcript expression inference. 

The “grch38_gencode38_vgrna_k32” folder contains a spliced reference graph and a pantranscriptome created using the GRCh38 reference genome and transcripts from the GENCODE (v38) annotation.

The “1kg_nygc_no001trio_af001_gencode38_k32” folder contains a spliced pangenome graph created using 1000 genomes project variants (New York Genome Center) and splice junctions from the GENCODE (v38) transcript annotation. The samples NA12878, NA12891 and NA12892 were excluded.   

The “minigraph_cactus_grch38_f1_clip_d9_m1k_D10M_m1k_cat_gencode38_vgrna_k32” folder contains a spliced pangenome graph and a pantranscriptome created using the allele-filtered minigraph cactus (MC) HPRC pangenome graph, and transcripts from both the CAT annotation on each HPRC assembly and the GENCODE (v38) annotation.

File types:

 “.xg”: Spliced pangenome graph (needed for vg mpmap and rpvg).

 “.gcsa”: GCSA index of spliced pangenome graph (needed for vg mpmap).

 “.gcsa.lcp”: LCP array used by GCSA index (needed for vg mpmap).

 “.dist”: Distance index of spliced pangenome graph (needed for vg mpmap).

 “.gbwt”: Pantranscriptome (needed for rpvg).

 “.gbwt.ri”: r-index of pantranscriptome (needed for rpvg).

 “.txt.gz”: Table with transcript and haplotype information for the haplotype-specific transcripts in the pantranscriptome (needed for rpvg).

Updates:

* 24/10/2022: Added pantranscriptomes and spliced reference

* 04/07/2022: Added graphs and indexes