Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.
Provides automated analysis pipelines for microbial genomics via a portable virtual machine (VM). CloVR aims to perform sophisticated analyses by using local resources and cloud computing platforms if additional resources are required for increased throughput. This software aims to reduce bottlenecks in sequence analysis by combining VMs and cloud computing and to simplify deployments of complex bioinformatics workflows by providing a single executable.
A classification system designed for metagenomics experiments that assigns taxonomic labels to short DNA reads. PhymmBL combines two components: (i) composition-directed taxonomic predictions from Phymm and (ii) basic local alignment search tool (BLAST)-based homology results. PhymmBL combines these to label each input sequence with its best guess as to the taxonomy of the source organism. Input sequences as short as 100 base pairs can be phylogenetically classified with PhymmBL more accurately than with any other existing method. PhymmBL predicts species, genus, family, order, class and phylum for each read, allowing users to arrange results according to levels of specificity relevant to their research goals.
Brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Anvi’o is an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. It empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. CONCOCT does unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples.
Uses tetranucleotide frequencies, differential coverage and read mapping information to bin assembled contigs. MetaWatt uses diamond blastx, hmmer and aragorn for quality control. Metawatt is very fast, runs on a normal pc or laptop and offers a graphical user interface for effective data exploration.
A software tool for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished.