:: 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
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kuhring M, Dabrowski PW, Piro VC, Nitsche A, Renard BY.
SuRankCo: supervised ranking of contigs in de novo assemblies.
BMC Bioinformatics. 2015 Jul 30;16:240. doi: 10.1186/s12859-015-0644-7. PMID: 26224355; PMCID: PMC4520199.
:: DESCRIPTION
TADA is a novel statistical method that utilizes inherited variation transmitted to affected offspring in conjunction with (de novo) mutations to identify risk genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Genet. 2013 Aug;9(8):e1003671. doi: 10.1371/journal.pgen.1003671.
Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.
He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.
:: DESCRIPTION
SeqCons (Sequence consensus) is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rausch, T., Koren, S., Gennady, D., Weese, D., Emde, A.-K., D?ring, A., Reinert, K. (2009).
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
Bioinformatics (2009) 25 (9): 1118-1124.
:: DESCRIPTION
The program triodenovo implemented a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Dec 21. pii: btu839.
A Bayesian framework for de novo mutation calling in parents-offspring trios.
Wei Q, Zhan X, Zhong X, Liu Y, Han Y, Chen W, Li B
:: DESCRIPTION
Ananas is an assembler for paired-end Illumina RNA-Seq reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Omega is a software for assembling and scaffolding Illumina sequencing data of microbial communities.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Omega: an Overlap-graph de novo Assembler for Metagenomics.
Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.
Bioinformatics. 2014 Jun 19. pii: btu395.
:: DESCRIPTION
PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 20.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA.
:: DESCRIPTION
NovoHMM is a software for hidden Markov model for de novo peptide sequencing.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Anal Chem. 2005 Nov 15;77(22):7265-73.
NovoHMM: a hidden Markov model for de novo peptide sequencing.
Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM.
:: DESCRIPTION
mirTrios was developed for identification and comprehensive analysis the de novo and rare inherited variants with one or multiple trios samples based on high-throughput sequencing data starting from a VCF file (version 4). It uses reference gene definitions and hg19 genomic coordinates for annotation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
N/A
:: MORE INFORMATION
Citation
mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing.
Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J.
J Med Genet. 2015 Apr;52(4):275-81. doi: 10.1136/jmedgenet-2014-102656.