Mercurial > repos > galaxy-australia > cactus_export
changeset 1:5c48d182d4fd draft
Deleted selected files
| author | galaxy-australia |
|---|---|
| date | Mon, 04 Apr 2022 06:09:17 +0000 |
| parents | 939be8401810 |
| children | 8d047c940e71 |
| files | README.rst help.md |
| diffstat | 2 files changed, 0 insertions(+), 76 deletions(-) [+] |
line wrap: on
line diff
--- a/README.rst Mon Apr 04 05:53:14 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -Cactus -====== - -This suite contains a wrapper for the -`Cactus <github.com/comparativeGenomicsToolkit/cactus>`__ whole-genome -aligner and another wrapper for exporting the data it generates. - -Requirements ------------- - -The developers provide an official Docker container. However, the Docker -container won’t run unless ``/etc/passwd`` is mounted (`see this -issue <https://github.com/ComparativeGenomicsToolkit/cactus/issues/677>`__). -Because of this, it is recommended to run Cactus using Singularity. - -Cactus uses a lot of RAM. We have tested it on Galaxy using 24 GB of RAM -for a progressive alignment of three chromosome-level, 150 megabase -genomes.
--- a/help.md Mon Apr 04 05:53:14 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ - -**What it does** - -[Cactus](https://github.com/ComparativeGenomicsToolkit/cactus) is a reference-free whole-genome multiple alignment program. -It can be used to progressively align a large number of genomes. - -**Usage** - -***Between-species mode*** - -If you are aligning genomes from **multiple species**, you need to provide a guide tree in Newick format. Cactus uses the guide tree to progressively align genomes, meaning that it doesn't need to align all possible pairs of genomes. - -A Newick-formatted tree for human, chimp and gorilla genomes looks like this: - -``` -(((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831); -``` - -The numbers are the branch lengths. - - -***Beta: Within-species mode*** - -You can also run Cactus in [pangenome mode](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) to align genomes of multiple individuals from the **same species**. -In this mode you will not be able to provide a guide tree. -Cactus will use [minigraph](https://github.com/lh3/minigraph) to generate a graph of the input genomes and then use the graph to order the alignments. -To use pangenome mode, select 'Within-species' in the 'Alignment mode' dropdown. - -**Input** - -The developers recommend soft-masking your genomes with RepeatMasker before running Cactus. -RepeatMasker is available on Galaxy. - -If you're using Between-species mode, you need to provide labels for the fasta files that match the leaves on the guide tree. -In the example above, you would use the label 'human' for the human fasta file. - -**Output** - -The main output of Cactus is in [HAL format](https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output). -You can use the [Cactus: export](root?tool_id=cactus_export) tool to convert the Cactus output to a VG or Multiple Alignment Format (MAF) file. - - ---- - -**What it does** - -Converts the HAL output from [Cactus whole-genome multiple sequence aligner](root?tool_id=cactus_cactus) into other formats. - -**Input** - -A [HAL file](https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output) from [Cactus](root?tool_id=cactus_cactus). - -**Output** - -Currently, you can export a pangenome in VG format, for use with [vg](https://github.com/vgteam/vg), and/or Multiple Alignment Format (MAF). -Note that MAF is **reference-based**, so it will contain alignments to a single reference from your list of inputs (i.e. not a graph). -By default, the first input genome will be used as the reference. -You can override this with the 'reference genome' option.