Jit
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Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2572 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...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2225 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...Filtlong: quality filtering tool for long reads
By Radha Agarkar 1653 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2285 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1405 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2225 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2283 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...3d-dna: 3D de novo assembly (3D DNA) pipeline
By Jit 2520 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 2398 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 2361 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...
