Installed This software should be available with no extra configuration. sweepfinder2 A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation. Please cite the following manuscript if using this software: M DeGiorgio, CD Huber, MH Hubisz, I Hellmann, R Nielsen (2016) SweepFinder2: increased sensitivity, robustness, and flexibility. Bioinformatics 32:1895-1897. Link to manual Link to the pdf manual

Conda See the ‘activating the conda environment’ section below to access this software. qiime2-2023.2 QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: Integrated and automatic tracking of data provenance Semantic type system Plugin system for extending microbiome analysis functionality Support for multiple types of user interfaces (e.

Conda See the ‘activating the conda environment’ section below to access this software. trinity-2.15.1 RNA-Seq De novo Assembly Using Trinity Quick Guide for the Impatient Trinity assembles transcript sequences from Illumina RNA-Seq data. Assemble RNA-Seq data like so: Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G Find assembled transcripts as: ‘trinity_out_dir/Trinity.fasta’ Use the documentation links in the right-sidebar to navigate this documentation, and contact our Google group for technical support.

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.