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SeqSphere+
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 sequence data. SeqSphere+ is the solution for easy and automated microbial analysis; enabling your lab to employ whole genome microbial typing (MLST+), traditional MLST or eMLST/rMLST sequencing projects. With fast and affordable microbial whole genome shotgun (WGS) next generation sequencing and automatized software analysis, microbiologists can use genome-wide hundreds/thousands of genes (core genome MLST or MLST+) for typing, resulting in higher discrimination and more accurate strain typing. The heightened discrimination power of MLST+, coupled with rapid and simple workflow NGS, makes this complete solution ideal for everyday microbial monitoring to outbreak investigation.
CheckM
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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 collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.
CGAL
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 in the absence of a ground truth. This software separates reads with no end or one end mapped and reads with ends mapped to different scaffolds if needed, and the alignment follows a striped implementation of the Smith-Waterman algorithm. It can be applied for the optimization and comparison of assembly algorithms.
BUSCO / Benchmarking Universal Single-Copy Orthologs
Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of benchmarking universal single-copy orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria.
KAT / K-mer Analysis Toolkit
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 error profiling, assessing sequencing bias and identifying contaminants and de novo genome assembly QC and validation. KAT is a C++11 application containing multiple tools, each of which exploits multi-core machines via multi-threading where possible. Core functionality is contained in a library designed to promote rapid development of new tools.
RAMPART
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. After assembling contigs using different tools and parameters, it produces statistics and plots enabling the user to interpret, compare and visualise results. Rampart uses metrics based on this information to assign scores to each assembly, highlighting which set of assembled contigs should be considered for further scaffolding and enhancement. This methodology enables rampart to evaluate its final assembly in the absence of a reference.
DOGMA / DOmain-based General Measure for transcriptome and proteome quality Assessment
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 information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. It achieves similar completeness scores as existing programs, but is able to run much faster when it is used in combination with a fast domain annotation tool such as UProC.
gEVAL
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 and assist in strategizing potential solutions for these issues. This facilitates the improvement of overall assemblies to a “gold” standard for release as reference genomes. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.
CES / Combined Error Score
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 candidate variants, separating true positive from false-positive markers. It performs in two steps: first, the program computes noise estimators’ empirical distributions and records it into a Local Genome Profile (LGP). Then, the software uses the pre-computed model for evaluating the region of interest.
SCAN / Sequence Comparative Analysis using Networks
Statistically compares distinct assemblies. SCAN is designed to compare the topological properties of two node sets in networks, and can make statistical comparisons on any network graph regardless of what the nodes represent. The software utilizes distinct features of sequence similarity networks to make statistical comparisons among assemblies using one or several reference organisms. It can be used at the network level to identify networks that are significantly similar to the reference across all the connected components in that network.
misFinder
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 uses the reference (or close related reference) to find the differences between the scaffolds and the reference, and uses multiple features extracted from the paired-end reads to validate these differences to determine whether they are assembly errors or correct assemblies corresponding to structural variations. misFinder is based on BLASTN, assembly (contigs/scaffolds), genome reference and paired-end reads from Solexa sequencing technology are its input, with aims to identify the mis-assemblies i.e., the assembly errors, and correct these errors to increase the accuracy of the assembly. It consists of three major steps: (1) Identify the differences between scaffolds and reference using BLASTN alignment; (2) Compute the breakpoints according to paired-end reads alignment information; (3) Validate the differences according to paired-end reads alignment information to distinguish the assembly errors and correct assemblies corresponding to structural variations.
U50
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 better assessment of assembly output. This program removes overlapping sequence of multiple contigs by utilizing a mask array, so the performance of the assembly is only measured by unique contigs. The U50 assembly metric is a tool to be used in conjunction with the commonly used N50, L50, and NG50 metrics. When used in unison, it gives a clearer picture of the performance and accuracy of the overall assembly.
iWGS / in silico Whole Genome Sequencer and Analyzer
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 generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools.
CAMSA / Comparative Analysis and Merging of Scaffold Assemblies
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 comprehensive comparative report for them. The report not only contains multiple numerical characteristics for the input assemblies, but also provides an interactive framework for their visual comparison and analysis. CAMSA also computes a merged assembly, combining the input assemblies into more comprehensive one, which resolves conflicts and determine orientation of unoriented scaffolds in the most confident way.
DraGnET / Draft Genome Evaluation Tool
Assists users in handling of annotated data. DraGnET provides an open source platform, available as both a web application and a standalone software, that allows users to store and curate unpublished annotated draft and complete genome data. The application contains functionalities for data access, searching, and modification as well as a basic local alignment search tool for performing amino acid sequence similarity searches and cross strain comparisons.
BACCardI
Obsolete
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 circular mode, representing a whole genome assembly of a prokaryotic genome, and (2) the linear mode, allowing a detailed analysis of a specific genomic region. This tool permits genome comparison via mapping of large insert clone libraries onto related genomes and finishing support.
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