Galaxy |

Cactus: export (version 2.7.1+galaxy0)

HAL file:

Multiple-genome alignment generated by Cactus

Output format:

The type of output you want to export. Run this tool once for each output format.

Reference genome:

Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'.

What it does

Converts the HAL output from Cactus whole-genome multiple sequence aligner into other formats.

Input

A HAL file from Cactus.

Output

Currently, you can export a pangenome in VG format, for use with vg, or Multiple Alignment Format (MAF). Note that these files are reference-based, so it will contain alignments to a single reference from your list of inputs (i.e. not a graph). You have to provide this with the ‘reference genome’ option.

You can also export an Assembly Hub for use with the UCSC Genome Browser.