Jit
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NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2253 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...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 2067 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 168 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2853 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...SKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2670 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2622 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1388 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2991 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...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 3042 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS...
By BioJoker 2524 days agowww.nature.com - Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975
