Jit
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FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
By Jit 2146 days agohttps://fuma.ctglab.nl/ - FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic...Web Apollo: a web-based genomic annotation editing platform
By Jit 2819 days agogenomearchitect.github.io - Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2520 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH...
By Abhimanyu Singh 2317 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...NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
By Jit 1807 days agogithub.com - NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly...dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
By Jit 2879 days agocsbl.bmb.uga.edu - dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE. Similar resources on the web include CAZy database and CAT. All...ONT assembly and Illumina polishing pipeline
By Jit 2701 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2666 days agogithub.com - This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2543 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2507 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...
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