:: 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
SRAssembler is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
McCarthy TW, Chou HC, Brendel VP.
SRAssembler: Selective Recursive local Assembly of homologous genomic regions.
BMC Bioinformatics. 2019 Jul 2;20(1):371. doi: 10.1186/s12859-019-2949-4. PMID: 31266441; PMCID: PMC6604332.
:: DESCRIPTION
Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads.
::DEVELOPER
The Brendel Group @ Indiana University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dong, Q., Wilkerson, M.D. & Brendel, V. (2007)
Tracembler – software for in silico chromosome walking in unassembled genomes.
BMC Bioinformatics 8, 151.
:: DESCRIPTION
PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation.
::DEVELOPER
Yukiteru Ono ,Kiyoshi Asai ,Michiaki Hamada
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Jan 1;29(1):119-21. doi: 10.1093/bioinformatics/bts649.
PBSIM: PacBio reads simulator–toward accurate genome assembly.
Ono Y, Asai K, Hamada M.
:: DESCRIPTION
hapAssembly beats the previous best for the important Haplotype Assembly Problem. It is an approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 15;29(16):1938-45. doi: 10.1093/bioinformatics/btt349.
Exact algorithms for haplotype assembly from whole-genome sequence data.
Chen ZZ, Deng F, Wang L.
:: 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
PaKman is a scalable algorithm for generating genomic contigs on distributed memory machines.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.
:: DESCRIPTION
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.
::DEVELOPER
The Broad Institute, Cambridge, MA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Manfred G. Grabherr, Brian J. Haas, […], and Aviv Regev
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Nat Biotechnol. 2011 May 15; 29(7): 644–652. doi: 10.1038/nbt.1883
:: 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
EvalDNA uses machine-learning methods to integrate genome assembly quality metrics into a single comprehensive quality score.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MacDonald ML, Lee KH.
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
BMC Bioinformatics. 2021 Nov 27;22(1):570. doi: 10.1186/s12859-021-04480-2. PMID: 34837948.
