Skip to content

Software requirements

Jump to bottom
Ryan Wick edited this page Apr 3, 2024 · 21 revisions

Trycycler runs on macOS and Linux. It requires Python 3.6 to 3.10 (newer versions may cause issues with a package dependency). It also uses a few Python packages (Edlib, NumPy and SciPy) but these should be taken care of by the installation process.

There are two general ways you can go about installing Trycycler:

  • Via conda. This has the advantage of taking care of external software dependencies for you, so if you want to go down this road, you can skip ahead to Installing with conda (i.e. you don't need to keep reading this page).
  • Via pip and Git. If you go down this road, then you'll need to ensure external dependencies are installed before you continue, so read on.

External tool dependencies

Trycycler also requires a few external tools to run. Install these by following the instructions on their websites or by using a package manager such as Homebrew or APT.

Miniasm

Miniasm is a very fast long-read assembly tool. Trycycler subsample uses it to perform a quick-and-dirty genome assembly for the purposes of estimating genome size.

To verify that you have miniasm installed, try running this command:

miniasm

If you see its usage instructions printed to the terminal, it's installed!

Minimap2

Minimap2 is a sequence alignment tool. It excels at many things, including aligning long reads to a reference.

To verify that you have minimap2 installed, try running this command:

minimap2 --help

If you see its usage instructions printed to the terminal, it's installed!

Mash

Mash is a tool for quickly estimating the similarity between sequences using k-mers.

To verify that you have Mash installed, try running this command:

mash --help

If you see its usage instructions printed to the terminal, it's installed!

R with phylogenetics packages

Trycycler cluster runs an R script to generate a phylogenetic tree. The ape and phangorn packages are required.

To verify that you have these installed, try opening up an R terminal:

R

And then try to load the ape and phangorn packages:

library(ape)
library(phangorn)

If these load without error, then you're good to go! Otherwise, install them in R:

install.packages("ape")
install.packages("phangorn")

MUSCLE

MUSCLE is a tool for multiple sequence alignment. Trycycler was developed with MUSCLE v3.8, and while Trycycler might work with MUSCLE v5 (released in late 2021), using the older version is strongly recommended (read more here).

To verify that you have MUSCLE installed, try running this command:

muscle

If you see its usage instructions printed to the terminal, it's installed!

Assemblers

Aside from miniasm (see above), Trycycler does not itself require any particular genome assemblers, but you will need to use assemblers to generate Trycycler's input assemblies.

Which you use is up to you, but some of my favourites are:

You might also want to install these tools to support other aspects of the assembly process:

If you're using a PacBio sequencer, then you could also install the SMRT Link software so you can use their Microbial Assembly pipeline.

Phylogenetic tree viewer

Trycycler does not need a tree viewer to run, but you'll probably want one to help you interpret Trycycler cluster results.

Anything that can view a Newick tree will do, such as one of the following:

Clone this wiki locally