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.
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.