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Microbial strain identification

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QIIME
Desktop

QIIME Quantitative Insights Into Microbial Ecology

An open source software package for comparison and analysis of microbial…

An open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data.

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LSA
Desktop

LSA Latent Strain Analysis

Allows metagenomic read partitioning. LSA can cluster sequences in fixed memory…

Allows metagenomic read partitioning. LSA can cluster sequences in fixed memory by using covariance information. It is able to separate sequences from related genomes into different partitions. The…

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ConStrains
Desktop

ConStrains Conspecific Strains

An open-source algorithm that identifies conspecific strains from metagenomic…

An open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. ConStrains uses single-nucleotide…

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PanPhlAn
Desktop

PanPhlAn Pangenome-based Phylogenomic Analysis

Uses metagenomic data to achieve strain-level microbial profiling resolution.…

Uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain level population genomic study of human-associated…

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Sigma
Desktop

Sigma Strain-level Inference of Genomes from Metagenomic Analysis

Identifies and quantifies genomes. Sigma uses the read mapping approach. It…

Identifies and quantifies genomes. Sigma uses the read mapping approach. It provides the statistical framework for hypothesis testing and confidence interval estimation. The tool permits maximum…

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DESMAN
Desktop

DESMAN De novo Extraction of Strains from MetAgeNomes

Allows user to extract strains from metagenomes. DESMAN is a program for…

Allows user to extract strains from metagenomes. DESMAN is a program for resolving both strain haplotypes and variations in gene content directly from short-read shotgun metagenome data. It detects…

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microbeGPS
Desktop

microbeGPS

Identifies microbial organisms in metagenomic sequencing data, estimates their…

Identifies microbial organisms in metagenomic sequencing data, estimates their abundance, and quantifies their distances to known reference genomes. MicrobeGPS is a bioinformatics software for the…

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HOMINID
Desktop

HOMINID HOst-Microbiome INteraction IDentification

A Python MPI program to identify associations between host genetic variation…

A Python MPI program to identify associations between host genetic variation and microbiome taxonomic composition. HOMINID is a computational approach based on Lasso linear regression, that given…

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VizBin
Desktop

VizBin

A Java based application which offers efficient and intuitive…

A Java based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning.…

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DUDes
Desktop

DUDes

A reference-based taxonomic profiler that introduces a novel top-down approach…

A reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic NGS samples. Rather than predicting an organism presence in the sample based only on relative…

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SPARSE
Desktop

SPARSE Strain Profiling and Analysis with Representative Sequence

Allows users to analyze and predict strain. SPARSE is a taxonomic program that…

Allows users to analyze and predict strain. SPARSE is a taxonomic program that indexes all genomes in large reference databases such as RefSeq into hierarchical clusters based on different sequence…

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StrainPhlAn
Desktop

StrainPhlAn

Tracks individual strains across large set of samples. StrainPhlAn is a…

Tracks individual strains across large set of samples. StrainPhlAn is a computational tool for performing metagenomic strain-level population genomics on large metagenomic datasets by profiling…

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microbiomeGWAS
Desktop

microbiomeGWAS

Tests the main effect or the single nucleotide polymorphism (SNP) environment…

Tests the main effect or the single nucleotide polymorphism (SNP) environment interaction for each SNP. MicrobiomeGWAS is a software package for identifying host genetic variants associated with…

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TaxIt
Desktop

TaxIt

Allows users to identify strain level of microbial tandem mass spectrometry…

Allows users to identify strain level of microbial tandem mass spectrometry (MS/MS).

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