Installed This software should be available with no extra configuration. nextdenovo-2.5.2 NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try NextPolish. We benchmarked NextDenovo against other assemblers using Oxford Nanopore long reads from human and Drosophila melanogaster, and PacBio continuous long reads (CLR) from Arabidopsis thaliana.

Conda See the ‘activating the conda environment’ section below to access this software. plotsr-0.5.4 Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies. See the readme for examples and to get example data. syri syri is included in the conda environment so that the alignmetns can be done. Activating the conda environment Check out a node with qrsh and run:

Conda See the ‘activating the conda environment’ section below to access this software. liftofftools-0.4.4 LiftoffTools is a toolkit to compare genes lifted between genome assemblies. Specifically it is designed to compare genes lifted over using Liftoff although it is also compatible with other lift-over tools such as UCSC liftOver as long as the feature IDs are the same. LiftoffTools provides 3 different modules. The first identifies variants in protein-coding genes and their effects on the gene.

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.