BOL

www.weizmann.ac.il - Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs...

github.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...

www.genomicus.bio.ens.psl.eu - Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it...

github.com - HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order...

minia.genouest.org - Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn...

evomics.org - The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of Bowtie, the primary parameters of velvet, and the process...

sb.nhri.org.tw - A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in...

garm-meta-assem.sourceforge.net - The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux...

github.com - quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve...

www.homolog.us - If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard...