BOL

github.com - A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...

Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all. More at...

To decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655

github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...

pevsnerlab.kennedykrieger.org - DRAGON: Database Referencing of Array Genes Online SNOMAD: Standardization and Normalization of Microarray Data SNPduo: SNP Analysis Between Two Individuals SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios SNPscan: Data...

github.com - RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold merging

wiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...

rosalind.info - Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works. http://rosalind.info/problems/list-view/

sourceforge.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...