:: DESCRIPTION
Cerulean is a hybrid assembly using high throughput short and long reads
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna,
Cerulean: A hybrid assembly using high throughput short and long reads (WABI2013)
rXiv preprint arXiv:1307.7933.
:: DESCRIPTION
PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. Unlike conventional methods that analyze each sample separately and then merge the outcomes to create a unified set of meta-annotations, PsiCLASS takes a multi-sample approach, simultaneously analyzing all RNA-seq data sets in an experiment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Song L, Sabunciyan S, Yang G, Florea L.
A multi-sample approach increases the accuracy of transcript assembly.
Nat Commun. 2019 Nov 1;10(1):5000. doi: 10.1038/s41467-019-12990-0. PMID: 31676772; PMCID: PMC6825223.
:: DESCRIPTION
The StriDe Assembler integrates string and de Bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions.
::DEVELOPER
Huang YT ythuang@cs.ccu.edu.tw.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Integration of String and de Bruijn Graphs for Genome Assembly.
Huang YT, Liao CF.
Bioinformatics. 2016 Jan 10. pii: btw011.
:: DESCRIPTION
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The MaSuRCA genome assembler.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.
Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476.
:: DESCRIPTION
SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111.
Efficient de novo assembly of large genomes using compressed data structures.
Simpson JT, Durbin R.
:: DESCRIPTION
SFA-SPA is a suffix array based short peptide assembler for metagenomic data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SFA-SPA: a suffix array based short peptide assembler for metagenomic data.
Yang Y, Zhong C, Yooseph S.
Bioinformatics. 2015 Jan 30. pii: btv052.
:: DESCRIPTION
Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
R. Chikhi, G. Rizk.
Space-efficient and exact de Bruijn graph representation based on a Bloom filter,
WABI 2012
:: DESCRIPTION
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li H.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19. PMID: 27153593; PMCID: PMC4937194.
:: DESCRIPTION
Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events, and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron and Ewan Birney
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts094
:: DESCRIPTION
VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
