Tutorial Instructions. Geneious Education tutorials are installed by either ‘ Dragging and dropping’ the zip file into Geneious or using File → Import → From File. Tutorial Last Updated Description Server Access Xanadu Cluster (SLURM) Oct Geneious: Loading data from the home directory, May , Mapping the . Explore the latest articles, projects, and questions and answers in Geneious, Please give me some recommendation as well as some tutorials link if you have.

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For instance there are various pre-defined lists of models, which are described in the manual. In most cases an optimum set of parameters for your data can be found using an iterative method. The critical inputs for Velvet Optimiser are the read files and the k-mer size search range.

There is a lot of information stored here, descriptions of what it all is can be found at the end of the PartitionFinder2 manual.

This maintains the paired ordering of the reads in the paired read files so the assembly software can use them correctly.

Adapter trimming This function trims adapters, barcodes and other contaminants from the yeneious. Steps involved and suggested tools: Gfneious end goal is to map some RNA-seq data to a genome iv’e been given bu Changing alignment formats can be a notorious pain, but luckily it’s made pretty simple by Geneious. Try running PartitionFinder2 with a smaller set of models e.

Error message using LASTZ in Geneious

Assembly of the reads. The ‘ models ‘ option defines which substitution models will be analysed for each partition. Failing to define codon positions in protein coding genes can lead to very poor estimates of phylogenetic trees. This tutorial might help if you are unsure about any particular aspect of your analysis, or you have never thought about partitioning schemes before. So, this is a “many This seems sensible, since we know that 2nd codon positions tend to evolve a lot more slowly than other codon positions.


You’ll get a list of options for the file format. If you’re using Windows, you’ll need to slightly modify section 4 – details are in the manual. The zebrafish genome was downloaded from UCSC and the other species’ sequence was generated using Illumina. All of the suggested tools for this protocol are installed and available.

Examine the draft contigs and assessment of the assembly quality.

This is by no means an exhaustive list. This file contains information on each of the models analysed for that subset, ranked in order of their Geneios score. It does affect the results sometimes, though usually not by much, and not in a way that usually affects the tree topology. Minimum read length Once all trimming steps are complete, this function yeneious sure that the reads are still longer than this value.

Sliding window trimming This function uses a sliding window to measure average quality and trims accordingly. Total number of reads – Gives you an idea of coverage.

See Trimmomatic website for detailed instructions.

PartitionFinder2 tutorial

You may get a slightly different result. We’re going to choose a small but sensible set of models. If you want to skip this step, you can just download the pre-formatted configuration file by clicking here. The ‘ alignment ‘ option tells PartitionFinder2 the name of the alignment, so here we’ll set this as follows: The suggested assembly software for this protocol is the Velvet Optimiser which wraps the Velvet Assembler.


What is de novo genome assembly? It can be difficult to know beforehand which of these options will be the best, but not all phylogenetics programs will allow for unlinked branchlengths. It can be run from within GVL Galaxy servers or by command line.

What happens with your contigs next is determined by what you need them for: See here for a comprehensive list of – and links to – short read assembly programs. For example, in medicine it can be used to identify, diagnose and potentially develop treatments for genetic diseases. The ttuorial of this section of the protocol is to show you how to understand your raw data, make informed decisions on how to handle it tjtorial maximise your chances geneiouss getting a good quality assembly.

Also note that if you change the model list for an analysis, PF2 will re-use any old results it has, so can be very quick. Some of the larger repeated elements such as the ribosomal RNA loci may not have all been resolved correctly. Some of the available assemblers include:. Convert the alignment to phylip format PartitionFinder2 works with phylip formatted alignments. There are a large number of short read assemblers available.

Now we have 7 data blocks defined.