:: DESCRIPTION
NN50-calculator (Normalized N50 calculator) is a tool for evaluating the correctness of genome assemblies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Oct 3;13:255. doi: 10.1186/1471-2105-13-255.
Normalized N50 assembly metric using gap-restricted co-linear chaining.
Mäkinen V, Salmela L, Ylinen J.
:: DESCRIPTION
FastMLST is a high speed standalone script wrote in Python3, which takes assemblies in FASTA format (gzipped is also allowed) and determines its ST according to MLST schemes defined in PubMLST.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Guerrero-Araya E, Muñoz M, Rodríguez C, Paredes-Sabja D.
FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies.
Bioinform Biol Insights. 2021 Nov 27;15:11779322211059238. doi: 10.1177/11779322211059238. PMID: 34866905; PMCID: PMC8637782.
:: DESCRIPTION
QUAST evaluates a quality of genome assemblies by computing various metrics and providing nice reports.
MetaQUAST evaluates and compares metagenome assemblies based on alignments to close references.
Icarus is a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on QUAST genome quality assessment tool
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Icarus: visualizer for de novo assembly evaluation.
Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A.
Bioinformatics. 2016 Jul 4. pii: btw379.
MetaQUAST: evaluation of metagenome assemblies.
Mikheenko A, Saveliev V, Gurevich A.
Bioinformatics. 2015 Nov 26. pii: btv697
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler
QUAST: quality assessment tool for genome assemblies
Bioinformatics volume 29, issue 8, pp. 1072-1075.
:: DESCRIPTION
The GMASS score is a novel measure for representing structural similarity between two assemblies. It represents the structural similarity of a pair of assemblies based on the length and number of similar genomic regions defined as consensus segment blocks (CSBs) in the assemblies.
::DEVELOPER
Bioinformatics Laboratory, Konkuk University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2019 Mar 18;20(1):147. doi: 10.1186/s12859-019-2710-z.
GMASS: a novel measure for genome assembly structural similarity.
Kwon D, Lee J, Kim J.
:: DESCRIPTION
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
Bao E, Jiang T, Girke T.
:: DESCRIPTION
Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.
DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Catchen J, Amores A, Bassham S.
Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.
G3 (Bethesda). 2020 Nov 5;10(11):4115-4128. doi: 10.1534/g3.120.401485. PMID: 32912931; PMCID: PMC7642942.
:: DESCRIPTION
BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
Bioinformatics. 2015 Jun 9. pii: btv351.
:: DESCRIPTION
Circlator is the first tool to automate assembly circularization and produce accurate linear representations of circular sequences.
::DEVELOPER
Pathogen Informatics, Wellcome Trust Sanger Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Circlator: automated circularization of genome assemblies using long sequencing reads.
Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR.
Genome Biol. 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0.
:: DESCRIPTION
rectangles is an ultimate tool for resolving repeats in genome assemblies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nikolay Vyahhi, Son K. Pham, Pavel Pevzner.
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly,
Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.
:: DESCRIPTION
GATB provides an easy way to develop efficient and fast NGS tools. GATB is a C++ library of high level functions designed to benefit from recent advances in NGS data structures for handling huge datasets of sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
GATB: Genome Assembly & Analysis Tool Box.
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D.
Bioinformatics. 2014 Jul 1. pii: btu406
