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fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2854 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...BEAP: Blast Extension and Assembly Program
By Shruti Paniwala 2826 days agowww.animalgenome.org - The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2230 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtOrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 1040 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2690 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2844 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2739 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3279 days agoStructural variation caller tools using long readsAndi
By Jit 3585 days agobioinformatics.oxfordjournals.org - This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient...Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical...
By BioStar 2054 days agowww.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...
