NAME
assembly_hub_constructor.pl - Build UCSC genome browser Assembly Hubs from genomic sequence and annotation
SYNOPSIS
assembly_hub_constructor.pl [--fa FILE] [--infolder PATH] [--out PATH] [--baseurl -URL] [options]
DESCRIPTION
The UCSC genome browser offers the possibility to visualize any organism (including organisms that are not included in the standard UCSC browser bundle) through hso called 'Assembly Hubs'. This script constructs Assembly Hubs from genomic sequence and annotation data.
OPTIONS
- --fa -f
-
Input file in Fasta format.
- --infolder -i
-
Directory which contains all track files in BED/bigBed format. The resulting Assembly Hub will contain these files in their respective bigFile version.
- --out -o
-
Destination folder for the output Assembly Hub.
- --baseurl -b
-
BaseURL used within the Assembly Hub. This URL will be included verbatim in the resulting Assembly Hub. It is crucial that this URl is valid, else the resulting Assembly Hub will be broken.
- --help -h
-
Print short help.
- --man
-
Prints the manual page and exits.
SEE ALSO
The UCSC Genome Wiki has extensive documentation for Assembly Hubs.