BioStar
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BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2696 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...HairSplitter: assembling long reads in an unknown number of haplotypes
By BioStar 1187 days agohal.archives-ouvertes.fr - Pros and cons of HairSplitter Limitations of HairSplitter: Not very fast: it re-polishes the whole assembly Limited in the number of haplotypes Strengths of HairSplitter: Very modular, can be used with any assembler Naive: makes no...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2983 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2839 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2853 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2738 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 2182 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2857 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...SvABA: Genome-wide detection of structural variants and indels by local assembly
By Abhimanyu Singh 2602 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....Free Genomics data !
By BioStar 2220 days agowww.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...
