### Graphs, pantranscriptomes and indexes

This folder contains different spliced pangenome graphs, pantranscriptomes and indexes. The graphs ending with “_genes” are exon-only splicing graphs. Pantranscriptomes ending with “_unidi” are unidirectional and should be used in rpvg if the reads are strand-specific. 

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:

* 03/25/2021: Added main graphs, pantranscriptomes and indexes

* 01/04/2022: Added HLA graph, pantranscriptome and indexes