Conda See the ‘activating the conda environment’ section below to access this software. GenomeScope 2.0: Reference-free profiling of polyploid genomes Many genomics analyses require first establishing a reference genome. However, de novo genome assembly is a complicated and computationally intensive process with many assumptions hidden to the user. A popular assessment prior to genome assembly is genome profiling, where the k-mer frequencies within the sequencing reads are analyzed to efficiently estimate major genome characteristics such as genome size, heterozygosity, and repetitiveness.
Configuration required See the relevant section below to configure this software before use. R-4.3.1 See the latest news here. R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Link to R FAQ from the r-project To activate this version of R Edit your $PATH to include /local/cluster/micromamba/envs/R-4.3.1/scripts. Setting up your R libraries You can use the pre-installed libraries without additional configuration.
Installed This software should be available with no extra configuration. interproscan-5.63 InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains. Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way.
Installed This software should be available with no extra configuration. flye-2.9.2 Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome assembly.
Conda See the ‘activating the conda environment’ section below to access this software. DRAM-1.4.6 DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases. DRAM is run in two stages.
Conda See the ‘activating the conda environment’ section below to access this software. Bakta 1.8.0: rapid & standardized annotation of bacterial genomes, MAGs & plasmids Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis. Description Comprehensive & taxonomy-independent database Bakta provides a large and taxonomy-independent database using UniProt’s entire UniRef protein sequence cluster universe.