The taxonomic classification of environmental 16S rRNA gene sequences is carried out by using either a homology-based or prediction-based approach. The former approach requires the alignment of a query 16S rRNA sequence with all the 16S rRNA sequences present in the reference database, such as Ribosomal Database Project, Greengenes and SILVA.
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.
Uses as a flexible tool for aligning sequences to a template alignment. PyNAST is a reimplementation of NAST (Nearest Alignment Space Termination), introducing new features that increase its portability and flexibility. Its availability as an open source application with three convenient interfaces will allow the application of the NAST algorithm on a wider basis, to larger datasets, and in novel domains. In this package, the user can specify an arbitrary template alignment in a standard fasta alignment file to which candidate sequences should be aligned.
Aligns and optionally taxonomically classifies ribosomal RNA (rRNA gene sequences). SINA is part of the rRNA gene processing pipeline of the SILVA ribosomal databases project. The software can execute a homology search based on the computed alignment and generate a per sequence classifications from the search results. It also allows to convert reference alignments from FASTA to ARB format. SINA was compared with the commonly used high throughput multiple sequence alignment (MSA) programs PyNAST and mothur.
Provides a suite for trans-omics approaches. ECOMICS is composed of four components: (i) E-class, for taxonomic classification of prokaryotic and eukaryotic DNA sequences, (ii) FT2B to process nuclear magnetic resonance (NMR) spectra for downstream chemical analyses, (iii) Bm-Char which perform an assignment of specific compounds in lignocellulose, and (iv) HetMap to identify and visualize heterogeneous data and correlation matrices.
Estimates genome relative abundance with shotgun metagenomic reads. GRAMMy is a unified Genome Relative Abundance (GRA) estimation framework based on a mixture model for the short metagenomic reads and an expectation maximization (EM) algorithm. The software provides users with a wide choice of mapping and alignment tools. It is especially suitable for short read datasets due to its handling of read assignment ambiguities.
A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching, and classification. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities.