SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer

Sequence Alignment/Map format: a comprehensive review of approaches and applications

The Sequence Alignment/Map (SAM) format file is the text file used to record alignment information. Alignment is the core of sequencing analysis, and downstream tasks accept mapping results for further processing. Given the rapid development of the sequencing industry today, a comprehensive understanding of the SAM format and related tools is necessary to meet the challenges of data processing and analysis. This paper is devoted to retrieving knowledge in the broad field of SAM. First, the format of SAM is introduced to understand the overall process of the sequencing analysis. Then, existing work is systematically classified in accordance with generation, compression and application, and the involved SAM tools are specifically mined. Lastly, a summary and some thoughts on future directions are provided.

The A, C, G, and T of Genome Assembly

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

TraV: a genome context sensitive transcriptome browser

Next-generation sequencing (NGS) technologies like Illumina and ABI Solid enable the investigation of transcriptional activities of genomes. While read mapping tools have been continually improved to enable the processing of the increasing number of reads generated by NGS technologies, analysis and visualization tools are struggling with the amount of data they are presented with. Current tools are capable of handling at most two to three datasets simultaneously before they are limited by available memory or due to processing overhead. In order to process fifteen transcriptome sequencing experiments of Bacillus licheniformis DSM13 obtained in a previous study, we developed TraV, a RNA-Seq analysis and visualization tool. The analytical methods are designed for prokaryotic RNA-seq experiments. TraV calculates single nucleotide activities from the mapping information to visualize and analyze multiple transcriptome sequencing experiments. The use of nucleotide activities instead of single read mapping information is highly memory efficient without incurring a processing overhead. TraV is available at http://appmibio.uni-goettingen.de/index.php?sec=serv.

Harnessing virtual machines to simplify next-generation DNA sequencing analysis

MOTIVATION

The growth of next-generation sequencing (NGS) has not only dramatically accelerated the pace of research in the field of genomics, but it has also opened the door to personalized medicine and diagnostics. The resulting flood of data has led to the rapid development of large numbers of bioinformatic tools for data analysis, creating a challenging situation for researchers when choosing and configuring a variety of software for their analysis, and for other researchers trying to replicate their analysis. As NGS technology continues to expand from the research environment into clinical laboratories, the challenges associated with data analysis have the potential to slow the adoption of this technology.

RESULTS

Here we discuss the potential of virtual machines (VMs) to be used as a method for sharing entire installations of NGS software (bioinformatic 'pipelines'). VMs are created by programs designed to allow multiple operating systems to co-exist on a single physical machine, and they can be made following the object-oriented paradigm of encapsulating data and methods together. This allows NGS data to be distributed within a VM, along with the pre-configured software for its analysis. Although VMs have historically suffered from poor performance relative to native operating systems, we present benchmarking results demonstrating that this reduced performance can now be minimized. We further discuss the many potential benefits of VMs as a solution for NGS analysis and describe several published examples. Lastly, we consider the benefits of VMs in facilitating the introduction of NGS technology into the clinical environment.

CONTACT

brian.wilhelm@umontreal.ca.

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

SUMMARY

Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are not suitable for alignment data in metagenomics, which are often interspecies alignments. We have developed a web browser-based desktop application for interactively visualizing alignment data of metagenomic sequences. This viewer is easy to use on all computer systems with modern web browsers and requires no software installation.

AVAILABILITY

http://weizhongli-lab.org/mgaviewer