Homology-Based Taxonomic Software Tools | Shotgun metagenomic sequencing data analysis
A majority of methods available for binning datasets obtained using shotgun sequencing belong to the taxonomy-dependent category. Based on the strategy used for comparing reads with sequences/pre-computed models, taxonomy-dependent methods can be sub-classified into alignment-based, composition-based and hybrid methods.
Allows users to taxonomically and functionally explore and analyze large-scale microbiome sequencing data. MEGAN is a comprehensive microbiome analysis toolbox for metagenome, meta-transcriptome, amplicon and from other sources data. Users can perform taxonomic, functional or comparative analysis, map reads to reference sequences, reference-based multiple alignments and reference-guided assembly and integrate their own classifications.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Programs search nucleotide databases by using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison. Users can select an optimization according to: (i) highly similar sequences, (ii) more dissimilar sequences or (iii) somewhat similar sequences. This web application proceeds by searching sets in NCBI data sources.
A method for phylogenetic analysis of metagenomic samples and for comparison of community structure among multiple related samples. PhyloSift leverages phylogenetic models of molecular evolution to provide high resolution detection of organisms in a metagenome. Our approach is based on well known statistical phylogenetic models, is amenable to Bayesian hypothesis testing, and uses name-independent and OTU-free analyses to provide higher resolution about microbial community assemblages (versus methods that rely on taxonomy or OTUs). As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
Estimates the relative abundance of microbial cells by mapping reads against a reduced set of clade-specific marker sequences. MetaPhlAn accurately profiles microbial communities and requires only minutes to process millions of metagenomic reads. This classifier compares each metagenomic read from a sample to this marker catalog to identify high-confidence matches. It finally compares metagenomic reads against this precomputed marker catalog using nucleotide BLAST searches in order to provide clade abundances for one or more sequenced metagenomes.