Jit
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Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 3076 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2912 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...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 2470 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2349 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...proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
By Jit 3199 days agogithub.com - proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to...Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation
By Jit 2033 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...VirMet
By Jit 3651 days agogithub.com - Watch out: only a few files are counted in coverage statistics. Full documentation on Read the Docs. A set of tools for viral metagenomics. virmet is called with a command subcommand syntax: virmet fetch --viral n, for example,...Metagenomics assembly workshop !!
By Jit 3461 days agodenbi-metagenomics-workshop.readthedocs.io - Welcome to the one-day metagenomics assembly workshop. This tutorial will guide you through the typical steps of metagenome assembly and binning. The Tutorial Data Set FastQC Quality Control Assembly Velvet Assembly MEGAHIT...Omega2: metagenome assembly pipeline
By Jit 3378 days agoomega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...Kanthida Lab !
Research Interest: Bioinformatics High-throughput and high-dimensional data analysis Microbiome data analysis (Main focus) Next-generation and third-generation sequencing data analysis for genomics Gene expression data...
