Jit
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FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
By Neel 2297 days agogithub.com - FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use...KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH...
By Abhimanyu Singh 2173 days agowww.kegg.jp - KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1762 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/vtGSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 1715 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1556 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...vsFilt: A tool to improve virtual screening by structural filtration of docking poses
By Neel 1460 days agobiokinet.belozersky.msu.ru - The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition,...JumboDB: tool for de Bruijn graph construction
By BioStar 1194 days agogithub.com - jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads into compressed de Bruijn...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 103 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
By Jit 2742 days agogithub.com - npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It...WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1157 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...
