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Rectangle Graph for Repeat Resolution in Genome Assembly
By Rahul Nayak 2522 days agobioinf.spbau.ru - Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module...Genome assembly stats plotting
By Jit 2460 days agogithub.com - A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig Scaffold/contig N50 and N90Assembly base composition, in...Earth BioGenome Project
By Jit 2404 days agoThe central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotesGMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2357 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...
ComparativeGenomics Exercise2
By Neel 2285 days agoCOMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP @ cbs.dtu.dk Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdfCHARLES SWANTON LAB
They are using the latest DNA sequencing technology to read the genetic makeup of cancer cells within tumours in ever greater detail, teasing out patterns of evolution (evolutionary rule books), cancer heterogeneity and working out what changes have...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2135 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High...
By Jit 2051 days agogithub.com - Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a...MGSE: Mapping-based Genome Size Estimation
By Shruti Paniwala 1772 days agogithub.com - MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script...U-Plot: Genome U-Plot sample implementation
By Rahul Nayak 1726 days agogithub.com - The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.
