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Assembly evaluation software tools | De novo genome sequencing data analysis

Evaluating the quality and reliability of a de novo assembly and of single contigs in particular is challenging since commonly a ground truth is not readily available and numerous factors may influence results. Source text: Kuhring et al., 2015.

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SeqSphere+
Desktop

SeqSphere+

It is designed for distributed work-groups (client/server model) and allows…

It is designed for distributed work-groups (client/server model) and allows automatic processing and analyzing of NGS (e.g., Illumina, Ion Torrent or PacBio) and Sanger capillary-electrophoresis…

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QUAST
Desktop

QUAST

It evaluates a quality of genome assemblies by computing various metrics and…

It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.

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KBase
Dataset

KBase KBase

Supplies an unified environment for predictive biology which gathers data…

Supplies an unified environment for predictive biology which gathers data tools, and their associated interfaces. KBase aims to ease creation, execution and collaboration around reproducible analyses…

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CheckM
Desktop

CheckM

Provides a set of tools for assessing the quality of genomes recovered from…

Provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. CheckM provides robust estimates of genome completeness and contamination by using…

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HiMMe
Desktop

HiMMe

Assesses next-generation sequencing (NGS) data reliability and detects errors…

Assesses next-generation sequencing (NGS) data reliability and detects errors and repairs them. HiMMe allows comparison of results from different assembly runs and provides statistical insight to…

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KAT
Desktop

KAT K-mer Analysis Toolkit

A user-friendly, extendible and scalable toolkit for rapidly counting,…

A user-friendly, extendible and scalable toolkit for rapidly counting, comparing and analysing k-mers from various data sources. The tools in KAT assist the user with a wide range of tasks including…

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Icarus
Web
Desktop

Icarus

A novel genome visualizer for accurate assessment and analysis of genomic draft…

A novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is…

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DOGMA
Desktop

DOGMA DOmain-based General Measure for transcriptome and proteome quality Assessment

A program for fast and easy quality assessment of transcriptome and proteome…

A program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides…

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gEVAL
Web

gEVAL

Allows the evaluation of genome assemblies through its tools and pre-computed…

Allows the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions…

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misFinder
Desktop

misFinder

Aims to identify the assembly errors with high accuracy in an unbiased way and…

Aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their misjoined positions to improve the assembly accuracy before downstream analysis. misFinder…

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CES
Desktop

CES Combined Error Score

Provides a statistical method for determining inconsistent patterns in genomic…

Provides a statistical method for determining inconsistent patterns in genomic regions. CES is a standalone software which combines quality control scores across samples and ranks the obtained…

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gVolante
Web

gVolante

Achieves a method of handy analysis execution without command line operation.…

Achieves a method of handy analysis execution without command line operation. gVolante is a web server designed to make the best use of the reference gene set core vertebrate genes (CVG) for more…

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U50
Desktop

U50

Identifies unique, target-specific contigs by using a reference genome as…

Identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to the N50 metric. U50 is a metric that provides a…

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misSEQuel
Desktop

misSEQuel

Enhances the quality of draft genomes by identifying misassembly errors and…

Enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. misSEQuel also fulfills the critical need for…

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BUSCO
Desktop

BUSCO Benchmarking Universal Single-Copy Orthologs

Provides measures for quantitative assessment of genome assembly, gene set, and…

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal…

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IonGAP
Web

IonGAP

A publicly available web platform designed for the analysis of whole bacterial…

A publicly available web platform designed for the analysis of whole bacterial genomes by using Ion Torrent sequence data. Besides assembly, IonGAP integrates a variety of comparative genomics,…

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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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CGAL
Desktop

CGAL

A package for computing genome assembly likelihoods. CGAL computes the…

A package for computing genome assembly likelihoods. CGAL computes the likelihood of reads with respect to the assembly and a statistical model which can be used as a metric for evaluating assemblies…

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REAPR
Desktop

REAPR Recognising Errors in Assemblies using Paired Reads

A tool that precisely identifies errors in genome assemblies without the need…

A tool that precisely identifies errors in genome assemblies without the need for a reference sequence.

CEGMA
Desktop

CEGMA Core Eukaryotic Genes Mapping Approach

A computational method for building a highly reliable set of gene annotations…

A computational method for building a highly reliable set of gene annotations in the absence of experimental data. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of…

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CAMSA
Desktop

CAMSA Comparative Analysis and Merging of Scaffold Assemblies

A software tool for comparative analysis and merging of two or more given…

A software tool for comparative analysis and merging of two or more given scaffold assemblies. CAMSA takes as an input two or more assemblies of the same set of scaffolds and generates a…

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SuRankCo
Desktop

SuRankCo

Analyzes the reliability of de novo assemblies on the contig level and thereby…

Analyzes the reliability of de novo assemblies on the contig level and thereby allows quality control and ranking prior to further downstream and validation experiments. SuRankCo relies on a machine…

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nucleotid.es
Dataset

nucleotid.es

Provides continuous, objective and reproducible evaluation of genome assemblers…

Provides continuous, objective and reproducible evaluation of genome assemblers using docker containers. nucleotid.es compares how different genome assemblers perform against a variety of test…

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iWGS
Desktop

iWGS in silico Whole Genome Sequencer and Analyzer

An automated pipeline for guiding the choice of appropriate sequencing strategy…

An automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data…

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isoblat
Desktop

isoblat

Evaluates the reliability and the quality of a genome assembly. isoblat uses…

Evaluates the reliability and the quality of a genome assembly. isoblat uses RNA and BLAT parsing output to verify the assessment of an assembly with a transcriptome versus genome alignment method.…

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FRCbam
Desktop

FRCbam

A capable of computing FRCurve from the alignment of the reads to the assembled…

A capable of computing FRCurve from the alignment of the reads to the assembled contigs.

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MaGuS
Desktop

MaGuS Map-Guided Scaffolding

A modular tool that uses a draft genome assembly, a genome map, and…

A modular tool that uses a draft genome assembly, a genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. Its use can be…

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CAVe
Algorithm

CAVe Contig Assembly Verifier

Checks the positioning of the restriction fragments from the assembled…

Checks the positioning of the restriction fragments from the assembled sequence. CAVe proceeds to a verification by a scoring system that enumerates and scores various pairings of assembly fragments…

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Tigmint
Desktop

Tigmint

Allows correction of misassemblies. Tigmint uses linked reads from 10x Genomics…

Allows correction of misassemblies. Tigmint uses linked reads from 10x Genomics Chromium for identifying misassemblies and improving the quality and contiguity of a de novo genome assembly.

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Anchor
Desktop

Anchor

A set of tools for making automated improvements to de novo assemblies. Anchor…

A set of tools for making automated improvements to de novo assemblies. Anchor currently includes two main modules: correction of erroneous single-nucleotide variants and small indels and…

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LAP
Desktop

LAP

A de novo probabilistic measure of assembly quality which allows an objective…

A de novo probabilistic measure of assembly quality which allows an objective comparison of multiple assemblies generated from a same set of reads.

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BACCardI
Desktop

BACCardI

Generates virtual clone maps. BACCardI allows the projection of read pair…

Generates virtual clone maps. BACCardI allows the projection of read pair information as obtained from positioning of end sequences onto the genome assembly. It offers two different modes: (1) the…

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ALE
Desktop

ALE Assembly Likelihood Estimator

A probabalistic framework for determining the likelihood of an assembly given…

A probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it.

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