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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1697 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2415 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2393 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...ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
By LEGE 229 days agogithub.com - ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2415 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 2603 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
By Abhimanyu Singh 2321 days agobioinfo-csi.nus.edu.sg - From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA...Comparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4142 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 2585 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2574 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...
