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SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
By Abhimanyu Singh 3361 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 3005 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3429 days agoStructural variation caller tools using long readsMulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 3303 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3169 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...A web-based tool for sequence alignment statistics and innovative visualization
By BioStar 853 days agobioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...String graph based genome assembly software and tools !
By Rahul Nayak 3150 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 3004 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...
Evaluation of genome assembly software based on long reads
By BioStar 2741 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...Software for genome assembly !
By LEGE 2166 days agoList of bioinformatics tools/Software Website References for genome assembly:
