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Reference-assisted assembly software tools | De novo genome sequencing data analysis

An alternative approach for scaffolding genomes relies on the use of a complete (closed) reference genome to guide the ordering and the orientating of the contigs. Many available methods exist for mapping (and then scaffolding) the generated draft…
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SPAdes
Desktop

SPAdes

A single-cell assembler for capturing and sequencing “microbial dark…

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes…

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Cufflinks
Desktop

Cufflinks

Assembles transcripts, estimates their abundances, and tests for differential…

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

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GAAP
Desktop

GAAP Genome-organization-framework Assisted Assembly Pipeline

A cGOF (core-gene-defined Genome-organization-framework) Assisted Assembly…

A cGOF (core-gene-defined Genome-organization-framework) Assisted Assembly Pipeline. GAAP is aimed at scaffolding and extending scaffolds and contigs based on de novo assembly of one paired-end…

Mauve
Desktop

Mauve

A system for constructing multiple genome alignments in the presence of…

A system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research…

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ALLMAPS
Desktop
Web

ALLMAPS

A method capable of computing a scaffold ordering that maximizes colinearity…

A method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally…

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Chromosomer
Desktop

Chromosomer

Automates reference-assisted building of genomic chromosomes. Chromosomer…

Automates reference-assisted building of genomic chromosomes. Chromosomer employs alignments between fragments to construct draft chromosomes. It maps fragments to a reference genome by using results…

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Multi-CAR
Web

Multi-CAR

Orders and orients the contigs of a draft genome by using multiple complete…

Orders and orients the contigs of a draft genome by using multiple complete genomes of related organisms as references. Multi-CAR was tested on a real dataset composed of several prokaryotic genomes.…

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DeNoGAP
Desktop

DeNoGAP De-Novo Genome Analysis Pipeline

Performs reference-assisted and de novo gene prediction, homolog protein family…

Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics…

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MITObim
Desktop

MITObim MITOchondrial Baiting and Iterative Mapping

An in silico approach for the reconstruction of complete mitochondrial genomes…

An in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping.…

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CSAR
Desktop

CSAR Contig Scaffolding tool using Algebraic Rearrangements

Orders and orients the contigs of a given draft genome based on a reference…

Orders and orients the contigs of a given draft genome based on a reference genome of a related organism. CSAR is a reference-based scaffolding application that uses algebraic rearrangements. This…

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HaploMerger
Desktop

HaploMerger

Improves genome assembly in the post-assembly stage. HaploMerger is an…

Improves genome assembly in the post-assembly stage. HaploMerger is an automated pipeline to resolve allelic relations in polymorphic diploid assembly and output the reference haploid assembly. It…

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Projector 2
Web

Projector 2

It was designed for automatic positioning of contigs from an unfinished…

It was designed for automatic positioning of contigs from an unfinished prokaryotic genome onto (parts of) a template genome of a closely related strain or species. Because increasing numbers of…

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AlignGraph
Desktop

AlignGraph

An algorithm for extending and joining de novo-assembled contigs or scaffolds…

An algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. AlignGraph aligns paired-end (PE) reads and preassembled contigs or…

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Ragout
Desktop

Ragout Reference-Assisted Genome Ordering UTility

A tool for assisted assembly using multiple references. It takes a short read…

A tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the…

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OneMap
Desktop

OneMap

Constructs linkage maps of outcrossing plant species, using full-sib families…

Constructs linkage maps of outcrossing plant species, using full-sib families derived from two outbred parents. OneMap analyses are performed using a novel methodology based on the maximum likelihood…

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MSTMap
Desktop
Web

MSTMap

A software tool that is capable of constructing genetic linkage maps…

A software tool that is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool…

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HighMap
Desktop

HighMap

Constructs high-density linkage maps from next-generation sequencing (NGS)…

Constructs high-density linkage maps from next-generation sequencing (NGS) data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a…

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SCARF
Desktop
Web

SCARF Scaffolded and Corrected Assembly of Roche 454

A next-generation sequence assembly tool for evolutionary genomics that is…

A next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The…

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ABACAS
Desktop

ABACAS

It is intended as a tool to rapidly contiguate (align, order, orientate),…

It is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is…

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OSLay
Desktop

OSLay

Uses synteny between matching sequences in a target assembly and a reference…

Uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight…

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r2cat
Desktop

r2cat related reference contig arrangement tool

It is able to quickly match a set of contigs onto a related genome, order the…

It is able to quickly match a set of contigs onto a related genome, order the contigs according to their matches and display the result in an interactive synteny plot. The matching, however, is not…

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CAR
Desktop
Web

CAR Contig Assembly of prokaryotic draft genomes using rearrangements

A reference-based contig assembly (or scaffolding) tool that can efficiently…

A reference-based contig assembly (or scaffolding) tool that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related…

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SIS
Desktop
Web

SIS

A linear-time algorithm that can generate a set of contig scaffolds for a draft…

A linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and…

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fillScaffolds
Desktop

fillScaffolds

Involves optimally filling in genes missing from the scaffolds, while…

Involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is…

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AMOScmp-shortRe…
Desktop

AMOScmp-shortReads-alignmentTrimmed

Permits to proceed alignment based trimming and to assemble short reads.…

Permits to proceed alignment based trimming and to assemble short reads. AMOScmp-shortReads-alignmentTrimmed is based on AMOScmp with several differences compared to the initial version. It includes…

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refseqget
Desktop

refseqget

Gets reference sequence. refseqget reads a reference sequence and returns the…

Gets reference sequence. refseqget reads a reference sequence and returns the data in one of the EMBOSS reference sequence formats.

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NovoAlign
Desktop

NovoAlign

Uses for mapping of short reads onto a reference genome from Illumina, Ion…

Uses for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms. NovoAlign is packed with unsurpassed features like alignment quality scores using posterior…

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RACA
Desktop

RACA Reference-Assisted Chromosome Assembly

An algorithm to reliably order and orient sequence scaffolds generated by NGS…

An algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of…

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CONTIGuator
Desktop
Web

CONTIGuator

Designed for the bacterial genomes finishing process. CONTIGuator is a software…

Designed for the bacterial genomes finishing process. CONTIGuator is a software that combines the routines of ABACAS with a contig profiling viewable with the Artemis comparison tool. The software…

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