In addition, they have become essential to many emerging sequencing technologies (454, Illumina-Solexa, etc)., which can generate very high coverage short reads data (from 30 bp up to 500 bp).
More recently, however, error has re-emerged as an important concern in sequence analysis, in part because errors occur at elevated rates in the reads produced by many next-generation sequencing technologies.
A simplistic approach to this problem would be to extend the seed until a mismatch occurs but this approach ignores both the additional information available in quality scores and the high error rate inherent in many high-throughput sequencing technologies.
Many next-generation sequencing technologies have been developed to answer important biological questions.
Cell-type-specific differential expression analysis will ultimately benefit many epigenomics-oriented sequencing technologies, such as DNA methylation, ChIP-seq, and histone modification profiling, thereby providing a deeper understanding of the molecular mechanisms operating at the level of specific cell types.
With advances in next-generation sequencing technologies, many genomes of Helicobacter isolates have been sequenced by many laboratories [ 18– 22].
While many applications of new sequencing technologies make use of mapped assemblies, de novo sequence assembly is still common.
However, read count is vulnerable to sequencing bias since the preparation steps in many of today's sequencing technologies produce cDNA fragments with positional bias [ 63].
Similar to sequencing technologies, many bioinformatics tools have also been developed for the short-read sequence data assembly and analysis, but the requisite knowledge is very limited.
With the advances in next-generation sequencing technologies, many genomes of Listeria spp. have recently been sequenced by researchers [ 2, 14].
