Builds an assembly config for a custom genome using the flat { name, uri }
shorthand: JBrowse itself picks the concrete adapter type
(IndexedFastaAdapter/BgzipFastaAdapter/TwoBitAdapter) from the extension,
derives the .fai/.gzi index locations, and fills in the reference sequence
track when the config loads, so only the FASTA URL is required and no
adapter-type table lives in R.
assembly(fasta, name = NULL, aliases = NULL, refname_aliases = NULL)URL to the sequence: a .fa/.fasta (optionally bgzipped) or a
.2bit. The adapter type is inferred from the extension by JBrowse.
Assembly name. Defaults to the FASTA file's base name.
Reference-name aliases for the assembly (e.g. "GRCh37").
URL to a reference-name alias table mapping e.g. 1
to chr1.
an assembly config list for JBrowseR()
For common human/model genomes you do not need this at all — pass a hub name
straight to JBrowseR() (e.g. JBrowseR("hg38")) and the assembly, reference
name aliases, cytobands, and gene-name search all come preconfigured.
assembly(
"https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
aliases = "GRCh37"
)
#> $name
#> [1] "hg19"
#>
#> $uri
#> [1] "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz"
#>
#> $aliases
#> $aliases[[1]]
#> [1] "GRCh37"
#>
#>