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      FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing

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      Mycological Progress
      Springer Nature

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          Next-generation transcriptome assembly.

          Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.
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            Quake: quality-aware detection and correction of sequencing errors

            We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.
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              Assembly of large genomes using second-generation sequencing.

              Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data. We also review the genomes that have been assembled recently from short reads and make recommendations for sequencing strategies that will yield a high-quality assembly.
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                Author and article information

                Journal
                Mycological Progress
                Mycol Progress
                Springer Nature
                1617-416X
                1861-8952
                August 2015
                July 2015
                : 14
                : 8
                Article
                10.1007/s11557-015-1077-4
                1f22d56c-57a8-422c-a1f7-3b8e576825f6
                © 2015
                History

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