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Assembly scaffolding software tools | De novo genome sequencing data analysis

The de novo assembly of short-read sequencing data usually leads to a fragmented set of genomic sequences (contigs). Ordering and orientating such contigs (scaffolding) represents the first, nontrivial step towards genome finishing and usually…
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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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PBSuite
Desktop

PBSuite

Affords a way for analysis of Pacific Biosciences long-read sequencing data.…

Affords a way for analysis of Pacific Biosciences long-read sequencing data. PBSuite is composed of two projects: PBJelly and PBHoney. The first one is an automated pipeline for aligning long…

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SOAPdenovo
Desktop

SOAPdenovo

Provides a short-read assembly method that can build a de novo draft assembly…

Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo is specially designed to assemble Illumina GA short reads. It creates new…

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SSPACE
Desktop

SSPACE

A stand-alone program for scaffolding pre-assembled contigs using NGS…

A stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance…

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Opera
Desktop

Opera Optimal Paired-End Read Assembler

A scalable, exact algorithm for the scaffold assembly of large, repeat-rich…

A scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, with consistent improvement over state-of-the-art programs for scaffold correctness and contiguity. OPERA provides…

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GOBOND
Desktop

GOBOND

A scaffolding program to deal with complicated genome. GOBOND allows to…

A scaffolding program to deal with complicated genome. GOBOND allows to assemble contigs from sequencing platforms. Pre-assembled contigs from one sequencing platform could be oriented and linked by…

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BOSS
Desktop

BOSS Building Optimized Scaffold graph for Scaffolding

Determines orientations and orders of contigs. BOSS employs a new statistical…

Determines orientations and orders of contigs. BOSS employs a new statistical method to decide whether an edge between contigs should be added and how the edge should be weighed. In addition, BOSS…

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GPM
Desktop

GPM Genome Puzzle Master

Enables the integration of additional genomic signposts to edit and build…

Enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules. GPM has the flexibility to edit…

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Architect
Desktop

Architect

A de novo scaffolder aimed at synthetic long read (SLR) technologies. Unlike…

A de novo scaffolder aimed at synthetic long read (SLR) technologies. Unlike previous assembly strategies, Architect does not require a costly subassembly step; instead it assembles genomes directly…

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pBACode
Desktop

pBACode

A random barcode based BAC library system. pBACode is a pool of Bacterial…

A random barcode based BAC library system. pBACode is a pool of Bacterial Artificial Chromosome (BAC) cloning vectors. It is able to introduce random sequences into BAC vectors so that each BAC clone…

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inGAP-sf
Desktop

inGAP-sf

Based on the combination of direct link and paired link graphs to address above…

Based on the combination of direct link and paired link graphs to address above scaffolding obstacles. inGAP-sf employs direct link to provide extra routes and decreases the complexity of repetitive…

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BugBuilder
Desktop

BugBuilder

Can carry out assembly and analysis of microbial genome sequences. BugBuilder…

Can carry out assembly and analysis of microbial genome sequences. BugBuilder takes sequence reads as inputs and produces submission-ready annotated genome assemblies, with ease-of-use prioritised to…

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MIP Scaffolder
Desktop

MIP Scaffolder

A program for scaffolding contigs produced by fragment assemblers using mate…

A program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.

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Scarpa
Desktop

Scarpa

A stand-alone scaffolding tool for NGS data. It can be used together with…

A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format.

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ScaffoldScaffol…
Desktop

ScaffoldScaffolder

A greedy heuristic algorithm to solve the weighted MAX-DIR problem. As a…

A greedy heuristic algorithm to solve the weighted MAX-DIR problem. As a heavier-weighted edge generally reflects greater confidence for the scaffolding which it represents, such an edge is likely to…

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GRASS
Desktop

GRASS GeneRic ASembly Scaffolder

A generic algorithm for scaffolding next-generation sequencing assemblies.

A generic algorithm for scaffolding next-generation sequencing assemblies.

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SOPRA
Desktop

SOPRA

Assembler for mate pair/paired-end reads from high throughput sequencing…

Assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.

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fragScaff
Desktop

fragScaff

Produces midrange scaffolding comparable to 40-kbp fosmid-based mate-pair…

Produces midrange scaffolding comparable to 40-kbp fosmid-based mate-pair libraries. fragScaff leverages coincidences between the content of different pools as a source of contiguity information.…

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FPSAC
Desktop

FPSAC Fast Phylogenetic Scaffolding of Ancient Contigs

Sequencing ancient genomes raises specific problems, because of the decay and…

Sequencing ancient genomes raises specific problems, because of the decay and fragmentation of ancient DNA among others, making the scaffolding of ancient contigs challenging. FPSAC is a general…

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FAST-SG
Desktop

FAST-SG Fast Scaffolding Graph

Allows users to build scaffolding graphs from short or long reads. FAST-SG is…

Allows users to build scaffolding graphs from short or long reads. FAST-SG is an open-source software which aims to speed up graphs’ construction by using moderate computational resources and to…

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ScaffMatch
Desktop

ScaffMatch

An efficient scaffolding algorithm that is able to handle reads with both short…

An efficient scaffolding algorithm that is able to handle reads with both short (<600 bp) and long (>35000 bp) insert sizes producing high-quality scaffolds. The ScaffMatch software…

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MeDuSa
Desktop
Web

MeDuSa Multi-Draft based Scaffolder

An algorithm for genome scaffolding. MeDuSa exploits information obtained from…

An algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs.…

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RAMPART
Desktop

RAMPART

A pipeline for creating multiple assemblies and a framework for analysing and…

A pipeline for creating multiple assemblies and a framework for analysing and comparing them. Rampart supports a variety of third-party tools for assembling, scaffolding and read error correction.…

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FinisherSC
Desktop

FinisherSC

A repeat-aware and scalable tool for upgrading de-novo assembly using long…

A repeat-aware and scalable tool for upgrading de-novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools…

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AGORA
Desktop

AGORA Assembly Guided by Optical Restriction Alignment

Uses optical map information directly within the de Bruijn graph framework to…

Uses optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided.

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BESST
Desktop

BESST Bias Estimating Stepwise Scaffolding Tool

A package for scaffolding genomic assemblies. BESST contains several modules…

A package for scaffolding genomic assemblies. BESST contains several modules for e.g. building a "contig graph" from available information, obtaining scaffolds from this graph, and accurate…

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scaffold_builde…
Desktop
Web

scaffold_builder

The abundance of repeat elements in genomes can impede the assembly of a single…

The abundance of repeat elements in genomes can impede the assembly of a single sequence. The tool Scaffold_builder was designed to generate scaffolds (super contigs of sequences joined by N-bases)…

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ARCS
Desktop

ARCS Assembly Roundup by Chromium Scaffolding

Utilizes the barcoding information contained in linked reads to further…

Utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. ARCS leverages the rich information content of high-volume long…

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SWALO
Desktop

SWALO Scaffolding With Assembly Likelihood Optimization

A package for scaffolding based on likelihood of genome assemblies computed…

A package for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. SWALO learns parameters automatically from the data. It is also able to make use of…

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WiseScaffolder
Desktop
Web

WiseScaffolder

A standalone semi-automatic application for genome scaffolding of pre-assembled…

A standalone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. WiseScaffolder also produces editable scaffold maps, allowing either to build gapped…

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ConPath
Desktop

ConPath

Determines the longest scaffolds. ConPath exploits mate-pair information to…

Determines the longest scaffolds. ConPath exploits mate-pair information to construct scaffolds by ordering and orienting separate sequence contigs. It provides various useful viewers and dialogue…

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SLIQ
Desktop

SLIQ

Predicts relative positions and orientations of the contigs, yielding a…

Predicts relative positions and orientations of the contigs, yielding a directed contig graph. SLIQ provides a set of simple linear inequalities derived from the geometry of contigs on the line. It…

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AGOUTI
Desktop

AGOUTI Annotated Genome Optimization Using Transcriptome Information

Uses RNA-seq data to simultaneously combine contigs into scaffolds and…

Uses RNA-seq data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the…

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TGNet
Desktop

TGNet Transcript to Genome Consistency Network

Generates tables for visualization in Cytoscape from FASTA sequence and…

Generates tables for visualization in Cytoscape from FASTA sequence and scaffolding information files. TGNet contains scripts that evaluates genome scaffolding by aligning independently obtained…

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SILP2
Desktop

SILP2 Scaffolding using Integer Linear Programming

A scalable scaffolding tool based on explicit formalization of likelihood…

A scalable scaffolding tool based on explicit formalization of likelihood maximization as the optimization objective. SILP2 is able to scaffold large mammalian genomes, resulting in the longest and…

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FASSI
Desktop

FASSI Fingerprint and ASSembly Incorporation

Calculates bacterial artificial chromosome (BAC) end length constraints from…

Calculates bacterial artificial chromosome (BAC) end length constraints from clone fingerprint map contigs created by the FPC package. FASSI aims to improve the contiguity of whole-genome shotgun…

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LINKS
Desktop

LINKS Long Interval Nucleotide K-mer Scaffolder

A genomics application for scaffolding or re-scaffolding genome assemblies with…

A genomics application for scaffolding or re-scaffolding genome assemblies with imperfect, long reads. LINKS provides a generic framework for scaffolding and can work on any sequences.

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Atlas-Link
Desktop

Atlas-Link

The software implements a greedy algorithm and uses graph theory to link and…

The software implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information.

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SSPACE-LongRead
Desktop

SSPACE-LongRead

A stand-alone program for scaffolding pre-assembled contigs using long reads…

A stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Using the long read information, contigs (or scaffolds) are placed in the right order and…

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AHA
Desktop

AHA

Contigs from a draft assembly generated by a different assembler can be joined…

Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.

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SWiPS
Desktop

SWiPS Scaffolding With Protein Sequences

Uses orthologous proteins to improve low quality genome assemblies. SWiPS is an…

Uses orthologous proteins to improve low quality genome assemblies. SWiPS is an algorithm that uses protein sequences to order and orient contigs into scaffolds, thus improving assembly contiguity…

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GenMapDB
Dataset

GenMapDB

Contains mapped large DNA fragments that span eight human chromosomes at…

Contains mapped large DNA fragments that span eight human chromosomes at ∼1-Mb resolution. GenMapDB is useful in a wide range of applications from microarray-based gene mapping to identification of…

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