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Assembly software tools | Shotgun metagenomic sequencing data analysis

Most currently available assemblers were designed to assemble individual genomes or, in some cases, genomes of polyploid eukaryotes; however, they were not designed to assemble metagenomes comprising multiple species with nonuniform sequence…
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Orione
Web

Orione

A Galaxy-based framework consisting of publicly available research software and…

A Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology…

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MGS Canopy…
Desktop

MGS Canopy Algorithm

Enables comprehensive discovery of new microbial organisms, viruses and…

Enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities. MGS Canopy Algorithm aids to assembly microbial genomes without the need for reference…

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MetAMOS
Desktop

MetAMOS

Allows metagenomic assembly and analysis. MetAMOS is a modular and customizable…

Allows metagenomic assembly and analysis. MetAMOS is a modular and customizable framework providing a pushbutton solution for analysis of metagenomic datasets, irrespective of the sequencing…

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Ray Meta
Desktop

Ray Meta

A massively distributed metagenome assembler that is coupled with Ray…

A massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.

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MetaVelvet
Desktop

MetaVelvet

We modified and extended a single-genome and de Bruijn-graph based assembler,…

We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly.

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IDBA-UD
Desktop

IDBA-UD

A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data…

A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

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MetaSort
Desktop

MetaSort

Recovers nearly complete genomes from metagenomic samples. MetaSort combines…

Recovers nearly complete genomes from metagenomic samples. MetaSort combines the advantages of traditional metagenomics and single-cell genomics. It is able to segregate small subsets of cells with…

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Snowball
Desktop

Snowball

A strain aware gene assembler for reconstruction of gene domains of interest…

A strain aware gene assembler for reconstruction of gene domains of interest from shotgun metagenomic data of microbial communities. Snowball performs gene assembly of individual gene domains based…

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Meta-IDBA
Desktop

Meta-IDBA

An iterative De Bruijn Graph De Novo short read assembler specially designed…

An iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly.

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PRICE
Desktop

PRICE Paired-Read Iterative Contig Extension

A software for the targeted de novo assembly of genomic sequence from…

A software for the targeted de novo assembly of genomic sequence from large-scale genomic or metagenomic datasets. PRICE is designed with paired-end data in mind but does not require such data. The…

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Phrap
Desktop

Phrap

Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses…

Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses a banded version of the Smith-Waterman-Gotoh algorithm to do pairwise comparisons of the sequences. It compares…

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BBAP
Desktop

BBAP BLAST-based assembly pipeline

Implements a unique BLAST-based greedy algorithm to assemble data set reads.…

Implements a unique BLAST-based greedy algorithm to assemble data set reads. BBAP is a BLAST-based assembly pipeline that provides multiple intuitive parameters, depending on the nature of the data…

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Bambus
Desktop

Bambus

A standalone assembler. Bambus relies on a combination of a novel method for…

A standalone assembler. Bambus relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic…

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MEGAHIT
Desktop

MEGAHIT

A NGS de novo assembler for assembling large and complex metagenomics data in a…

A NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. MEGAHIT finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and…

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Subtractive…
Desktop

Subtractive Assembly

A de novo assembly approach for comparative metagenomics that directly…

A de novo assembly approach for comparative metagenomics that directly assembles only the differential reads that distinguish between two groups of metagenomes. Using both simulated and real…

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MAP
Desktop

MAP Metagenomic Assembly Program

Allows assembly of reads generated from shot-gun sequencing (SGS). MAP is a…

Allows assembly of reads generated from shot-gun sequencing (SGS). MAP is a metagenomic assembly program for shotgun DNA reads, based on an improved overlap/layout/consensus (OLC) strategy…

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Xander
Desktop

Xander

Combines gene assignment with the rapid assembly of full-length or near…

Combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of…

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MetaQUAST
Desktop

MetaQUAST

A modification of QUAST, the state-of-the-art tool for genome assembly…

A modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (1) unknown…

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InteMAP
Desktop

InteMAP Integrated Metagenomic Assembly Pipeline

Integrates three assemblers, ABySS, IDBA-UD and CABOG, which were found to…

Integrates three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision of which assembling approaches to use according…

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Genovo
Desktop

Genovo

A novel de novo sequence assembler that discovers likely sequence…

A novel de novo sequence assembler that discovers likely sequence reconstructions under the model.

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GeneStitch
Desktop

GeneStitch

We present a novel way of using the de Bruijn graph assembly of metagenomes to…

We present a novel way of using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.

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MetaStorm
Web

MetaStorm

Offers both read matching and assembly-based annotation pipelines. MetaStorm is…

Offers both read matching and assembly-based annotation pipelines. MetaStorm is an online metagenomic analysis server. It enables customization of reference databases and allows users to upload…

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Faucet
Desktop

Faucet

Builds an assembly graph incrementally as each read is processed. Faucet is a…

Builds an assembly graph incrementally as each read is processed. Faucet is a 2-pass streaming algorithm for assembly graph construction. This algorithm is composed of an online phase and an offline…

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Athena
Desktop

Athena

Uses short-read barcodes to produce improved metagenomic assemblies. Athena is…

Uses short-read barcodes to produce improved metagenomic assemblies. Athena is an assembler that first uses an existing short-read assembler (SPAdes) to obtain an initial sequence covering of the…

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BIGMAC
Desktop

BIGMAC

Previous approaches have focused on pre-processing reads and optimizing…

Previous approaches have focused on pre-processing reads and optimizing assemblers. BIGMAC takes an alternative perspective to focus on the post-processing step. Using both the assembled contigs and…

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MetaVelvet-SL
Desktop

MetaVelvet-SL

An extension of the single-genome assembler Velvet. It has been proved to…

An extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo…

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Mapsembler
Desktop

Mapsembler

Processes large datasets of reads on commodity hardware. Mapsembler checks the…

Processes large datasets of reads on commodity hardware. Mapsembler checks the presence of a known piece of information with a bounded number of substitutions in a set of reads. It provides pieces of…

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Spherical
Desktop

Spherical

Proposes an iterative approach to assembling metagenomic datasets. Spherical…

Proposes an iterative approach to assembling metagenomic datasets. Spherical has been designed to produce a more complete assembly from deep sequenced metagenomic data. Utilization of multiple…

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BinSanity
Desktop

BinSanity

Utilizes the clustering algorithm affinity propagation to cluster assemblies…

Utilizes the clustering algorithm affinity propagation to cluster assemblies using coverage alone, removing potential composition based biases in clustering contigs. BinSanity uses composition data…

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Xgenovo
Desktop

Xgenovo

It generates quality assemblies with paired end reads.

It generates quality assemblies with paired end reads.

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Omega
Desktop

Omega overlap-graph metagenome assembler

Developed for assembling and scaffolding Illumina sequencing data of microbial…

Developed for assembling and scaffolding Illumina sequencing data of microbial communities.

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PANDAseq
Desktop

PANDAseq

Assembles paired-end reads rapidly and with the correction of most errors.

Assembles paired-end reads rapidly and with the correction of most errors.

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SAT-Assembler
Desktop

SAT-Assembler

A targeted gene assembly program which aims to recover gene families of…

A targeted gene assembly program which aims to recover gene families of particular interest to biologists.

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DIME
Desktop

DIME DIvide, conquer, and MErge

A metagenomic sequence assembly framework by taking the divide, conquer, and…

A metagenomic sequence assembly framework by taking the divide, conquer, and merge strategies. Two MapReduce implementations of DIME, DIME-cap3 and DIME-genovo are available. DIME offers great…

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metaSPAdes
Desktop

metaSPAdes

Addresses various challenges of metagenomics assembly by capitalizing on…

Addresses various challenges of metagenomics assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. metaSPAdes…

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MetaCAA
Desktop

MetaCAA Metagenomic assembly using a Clustering-Aided Approach

Employs a clustering-aided assembly procedure in order to achieve improved…

Employs a clustering-aided assembly procedure in order to achieve improved efficiency of contig assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters.…

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VALET
Desktop

VALET VALidating mETagenomic assemblies

Allows to perform de novo validation of metagenomic assemblies. VALET verifies…

Allows to perform de novo validation of metagenomic assemblies. VALET verifies a number of properties that should hold true for a correct assembly. If invariants are incorrect, they are reported one…

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assemblyget
Desktop

assemblyget

Get assembly of sequence reads. assemblyget is an Emboss tool that searches for…

Get assembly of sequence reads. assemblyget is an Emboss tool that searches for a sequence assembly and returns the data in one of the EBOSS assembly formats.

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MetaCompass
Desktop

MetaCompass

Consists in an effective assembly software package for the reference-assisted…

Consists in an effective assembly software package for the reference-assisted assembly of metagenomic data. MetaCompass can be useful for comparative metagenomics assembly and construction of…

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