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sourceforge.net - OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a...

decipher.cee.wisc.edu - DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page. To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the...

github.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...

http://genomeribbon.com/ - Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in...

github.com - LINKS is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads,...

github.com - SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. More at https://github.com/jts/sga SGA...

Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).

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...