Jit
Enthusiast computational biologist with business dream !!!
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The MARVEL assembler
By Jit 3074 days agogithub.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 2329 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2833 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
By Neel 2977 days agogithub.com - FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use...Scaffolding of a bacterial genome using MinION nanopore sequencing
By Rahul Agarwal 4106 days agowww.nature.com - Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot...NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
By Jit 3084 days ago Comments (1)github.com - CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning...Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
By Neel 2868 days agogithub.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful...1mb long DNA with Nanopore technology
By Jit 3210 days agoLongest read of 1mb achievements with NanoporeComparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4792 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopalcoursera genome assembly tutorial
By Jit 3235 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
