Evaluation of next-generation sequencing software in mapping and assembly

Abstract

Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.

Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau

“…Methyl coenzyme-M reductase is ubiquitous to methanogens and is crucial to the terminal step of methanogenesis where it is involved in the reduction of the methyl group bound to coenzyme-M (Denman et al, 2007). Though clone library analyses have some limitations in completely revealing the microbial compositions, development of high-throughput sequencing technologies such as MiSeq Sequencing offers the opportunity to obtain more accurate compositions of a microbial community (Bao et al, 2011).…”

Informatics and clinical genome sequencing: opening the black box

“…Projects such as ENCODE, the Encyclopedia of DNA Elements, 16,17 and the related GENCODE, encyclopedia of genes and gene variants, 18,19 aim to identify all functional elements in the human genome sequence and will ultimately be used to annotate all evidence-based gene features in the entire human genome at a high accuracy. Numerous programs have been developed specifically for genome assembly, alignment, and variant calling based on DNA sequence reads from high-throughput next-generation sequencing platforms 2,4,20,21 (Table 1). These include software developed for use with a particular sequencing platform, open access academic software with a variety of functionalities and platform compatibilities, and proprietary software designed for specific purposes such as diagnostics ( Table 2).…”

Avian transcriptomics: opportunities and challenges

“…There is a vast array of tools available for alignment and assembly of the sequences (Bao et al 2011;Trapnell and Salzberg 2009), which will be more or less suitable for the project in mind. If a reference genome or transcriptome is not available then the sequences will have to be assembled de novo, which requires special de novo assembly software (Haas and Zody 2010).…”