Jit
Enthusiast computational biologist with business dream !!!
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Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
By Jit 1817 days agoprakharg24.github.io - We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2844 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2992 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...Common steps for reads mapping !
By BioStar 1094 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.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...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...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2227 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2133 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...QuasR: Quantification and annotation of short reads in R
By Neel 1667 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...YAHA
By Jit 3333 days agowww.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....
