:: DESCRIPTION
ITMO Genome Assembler is a tool for de novo assembly of small and middle-sized genomes from reads, produced by Illumina/Solexa, Ion Torrent or Sanger sequencers.
::DEVELOPER
Computer Technologies Laboratory, National Research University of Information Technologies,
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
:: DESCRIPTION
PRICE (Paired-Read Iterative Contig Extension) is a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PRICE: Software for the Targeted Assembly of Components of (Meta)Genomic Sequence Data
J. Graham Ruby, Priya Bellare and Joseph L. DeRisi
G3 March 23, 2013 g3.113.005967
:: DESCRIPTION
The AssemblyD is a software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformation. 2013 Sep 23;9(16):840-1. doi: 10.6026/97320630009840. eCollection 2013.
AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras AA1, de Sá PH, Azevedo V, Silva A, Ramos RT.
:: DESCRIPTION
IMAP (the integrative meta-assembly pipeline) is a new software pipeline to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data.
::DEVELOPER
Bioinformatics Laboratory, Konkuk University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2019 Aug 27;14(8):e0221858. doi: 10.1371/journal.pone.0221858. eCollection 2019.
Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.
Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J.
:: DESCRIPTION
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
::DEVELOPER
Center for Algorithmic Biotechnology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA.
metaSPAdes: a new versatile metagenomic assembler.
Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15. PMID: 28298430; PMCID: PMC5411777.
hybridSPAdes: an algorithm for hybrid assembly of short and long reads.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA.
Bioinformatics. 2015 Nov 20. pii: btv688
Anton Bankevich,et al.
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021
:: DESCRIPTION
SWAP-Assembler (Small World Asynchronous Parallel model) is a scalable and fully parallelized genome assembler designed for massive sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.
Meng J, Wang B, Wei Y, Feng S, Balaji P.
BMC Bioinformatics. 2014;15 Suppl 9:S2. doi: 10.1186/1471-2105-15-S9-S2.
:: DESCRIPTION
PEAssember is a parallel de novo genome assembler for small – mid sized genomes.
::DEVELOPER
Pramila Nuwantha Ariyaratne, Sung Wing Kin, Ken
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.
PE-Assembler: de novo assembler using short paired-end reads.
Ariyaratne PN, Sung WK.
