Abhimanyu Singh
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Want to Know which genome assembler rule the world ?
Started by Rahul Agarwal 4121 days ago Replies (3) Last reply by Rahul Nayak 2151 days agoAssemblathon 2: evaluating de novo methods of genome...Bandage: interactive visualization of de novo genome assemblies
By Shruti Paniwala 2545 days agorrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2394 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2356 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2241 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2199 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1783 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 198 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1406 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Platanus
By Jit 3115 days ago Comments (1)platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the...
