Installed This software should be available with no extra configuration. PGA-20230303 General Introduction to PGA PGA (Plastid Genome Annotator), a standalone command line tool, can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach.

Conda See the ‘activating the conda environment’ section below to access this software. Configuration required See the relevant section below to configure this software before use. braker2 with genomethreader The CQLS has installed braker2 and genomethreader into a conda environment for you to use. In order for it to work, you will have to: Copy the augustus config directory using the script below Activate the conda environment You will be able to use the updated braker2, augustus, and genomethreader from within the conda environment.

Installed This software should be available with no extra configuration. iqtree2-2.2.0 Thanks to the recent advent of next-generation sequencing techniques, the amount of phylogenomic/transcriptomic data have been rapidly accumulated. This extremely facilitates resolving many “deep phylogenetic” questions in the tree of life. At the same time it poses major computational challenges to analyze such big data, where most phylogenetic software cannot handle. Moreover, there is a need to develop more complex probabilistic models to adequately capture realistic aspects of genomic sequence evolution.

Conda See the ‘activating the conda environment’ section below to access this software. STITCH-1.6.8 STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format. Activating the conda environment Check out a node using qrsh and run:

Conda See the ‘activating the conda environment’ section below to access this software. multiqc-1.14 MultiQC is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools. MultiQC doesn’t run other tools for you - it’s designed to be placed at the end of analysis pipelines or to be run manually when you’ve finished running your tools. When you launch MultiQC, it recursively searches through any provided file paths and finds files that it recognises.

Conda See the ‘activating the conda environment’ section below to access this software. Configuration required See the relevant section below to configure this software before use. funannotate-1.8.14 funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io Configuring the conda environment In order to use augustus with this software, you need to run the /local/cluster/conda/setup_funannotate_config.