MUMmer MUMmer is a system for rapidly aligning DNA and protein sequences. The nucmer aligner in the current version (release 4.x) can align two mammalian genomes in about 3 hours on a typical 32+ core workstation with 64+Gb RAM; smaller genomes such as bacteria or small eukaryotes are aligned in seconds or minutes. The promer utility generates alignments based upon the six-frame translations of both input sequences. promer permits the alignment of genomes for which the proteins are similar but the DNA sequence is too divergent to detect similarity.

Bactopia Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into three main parts: Bactopia Datasets, Bactopia Analysis Pipeline, and Bactopia Tools. Bactopia Datasets provide a framework for including many existing public datasets, as well as private datasets, into your analysis The process of downloading, building, and (or) configuring these datasets for Bactopia has been automated.

DIAMOND - Fast and sensitive protein alignment DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. Frameshift alignments for long read analysis. Low resource requirements and suitable for running on standard desktops or laptops. Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

SnpEff SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). SnpEff Summary A typical SnpEff use case would be: Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). Output: SnpEff analyzes the input variants.

InterProScan What is InterProScan? 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.

Conda See the ‘activating the conda environment’ section below to access this software. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) PICRUSt2 is a software for predicting functional abundances based only on marker gene sequences. Check out the paper here. “Function” usually refers to gene families such as KEGG orthologs and Enzyme Classification numbers, but predictions can be made for any arbitrary trait. Similarly, predictions are typically based on 16S rRNA gene sequencing data, but other marker genes can also be used.