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Taxonomy-independent methods (shotgun metagenomic analysis)

Taxonomy-independent methods for shotgun metagenomic analysis.

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CONCOCT
Desktop

CONCOCT Clustering cONtigs with COverage and ComposiTion

A program for unsupervised binning of metagenomic contigs by using nucleotide…

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…

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d2SBin
Desktop

d2SBin

Enables improvements of the contigs produced by existing binning tools. D2SBin…

Enables improvements of the contigs produced by existing binning tools. D2SBin calculates dissimilarity between contig and the bin’s center based on the Markov model of k-tuple sequence…

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SHERA
Desktop

SHERA SHortread Error-Reducing Aligner

Aligns each mate-pair to produce a composite read with Phred-like quality…

Aligns each mate-pair to produce a composite read with Phred-like quality scores. SHERA recalculates the error probability of each bp, given the base call data from both reads for nucleotides in the…

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MetaFast
Desktop

MetaFast METAgenome FAST analysis toolkit

Allows to represent a shotgun metagenome from an arbitrary environment as a…

Allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. MetaFast lies between the k-mer spectrum analysis and…

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MaxBin
Desktop

MaxBin

A software tool for binning assembled metagenomic sequences based on an…

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…

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MetaCluster-TA
Desktop

MetaCluster-TA

Allows to bin and annotate short paired-end reads. MetaCluster-TA is an…

Allows to bin and annotate short paired-end reads. MetaCluster-TA is an assembly-assisted approach which, instead of annotating each read or assembled contig separately, bins similar reads/contigs…

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TOSS
Desktop

TOSS TOol for Separating Short reads

Separates short paired-end reads from different organisms in a metagenomic…

Separates short paired-end reads from different organisms in a metagenomic dataset. TOSS uses abundance levels to proceed to the separation of genomes. It is able to separate unique l-mers from…

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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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MetaProb
Desktop

MetaProb

An assembly-assisted approach for reference-free metagenomic binning. MetaProb…

An assembly-assisted approach for reference-free metagenomic binning. MetaProb can deal with short and long reads in a novel probabilistic framework, by using probabilistic sequence signatures. We…

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COCACOLA
Desktop

COCACOLA

A general framework automatically bin contigs into OTUs based upon sequence…

A general framework automatically bin contigs into OTUs based upon sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real…

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MetaBAT
Desktop

MetaBAT

Integrates empirical probabilistic distances of genome abundance and…

Integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational…

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AbundanceBin
Desktop

AbundanceBin

An abundance-based tool for binning metagenomic sequences, such that the reads…

An abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances.

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PHYSCIMM
Desktop

PHYSCIMM PHY Sequence Clustering with Interpolated Markov Models

Allows to model clusters of sequences. PHYSCIMM uses interpolated Markov models…

Allows to model clusters of sequences. PHYSCIMM uses interpolated Markov models (IMMs). It was tested by clustering sequencing reads from an in vitro-simulated microbial community. The tool…

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MrGBP
Desktop

MrGBP Multi-resolution Genomic Binary Patterns

Extracts local ‘texture’ changes from nucleotide sequence data in image…

Extracts local ‘texture’ changes from nucleotide sequence data in image processing. MrGBP aims to extract local changes in numerical representations of genetic sequence data. To proceed, it…

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kmer project
Desktop

kmer project

Allows rapid estimation of pairwise dissimilarity between metagenomes. Though…

Allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel…

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MetaWatt
Desktop

MetaWatt

Uses tetranucleotide frequencies, differential coverage and read mapping…

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…

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Simka
Desktop

Simka

Computes a large collection of distances classically used in ecology to compare…

Computes a large collection of distances classically used in ecology to compare communities. Simka is a method able to calculate a full range of distances enabling the comparison of any number of…

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MyCC
Desktop

MyCC

An automated binning tool that combines genomic signatures, marker genes and…

An automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the…

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DectICO
Desktop

DectICO

An alignment-free supervised metagenomic classification method. The intrinsic…

An alignment-free supervised metagenomic classification method. The intrinsic correlation of oligonucleotides provides the feature set, which is selected dynamically using a kernel partial least…

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MBBC
Desktop

MBBC Metagenomic Binning Based on Clustering

A taxonomy-independent approach to cluster environmental shotgun reads, by…

A taxonomy-independent approach to cluster environmental shotgun reads, by considering k-mer frequency in reads and Markov properties of the inferred OTUs. Tested on twelve simulated datasets, MBBC…

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BiMeta
Desktop

BiMeta

A two-phase algorithm for the binning of metagenomic reads without using…

A two-phase algorithm for the binning of metagenomic reads without using reference genomes. Instead of directly clustering reads, the main idea of BiMeta is to provide an additional preprocessing…

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crAss
Web

crAss Cross-Assembly of Metagenomes

Metagenomes are often characterized by high levels of unknown reads with no…

Metagenomes are often characterized by high levels of unknown reads with no similarity to any sequences in Genbank. Although these are often discarded from analysis, they contain a wealth of…

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GroopM
Desktop

GroopM

A binning tool that primarily uses differential coverage to obtain high…

A binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. GroopM automatically bins contigs into discrete population genomes based…

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bwtCluster
Desktop

bwtCluster

Solves a number of core primitives in unsupervised metagenomic clustering using…

Solves a number of core primitives in unsupervised metagenomic clustering using just the bidirectional Burrows-Wheeler index and a union-find data structure on the set of reads. bwtCluster is an…

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CompostBin
Desktop

CompostBin

A DNA-composition-based binning algorithm for classifying metagenomic reads.

A DNA-composition-based binning algorithm for classifying metagenomic reads.

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TETRA
Desktop

TETRA

The standalone-programs can be used to calculate, how well tetranucleotide…

The standalone-programs can be used to calculate, how well tetranucleotide usage patterns in DNA sequences correlate.

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MetaObtainer
Desktop

MetaObtainer

Allows user to obtain the specified species from next-generation sequencing…

Allows user to obtain the specified species from next-generation sequencing (NGS) short reads. MetaObtainer uses overlap information to group short reads and then uses composition information to…

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