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We are analyzing https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-485.

Title:
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data | BMC Bioinformatics | Full Text
Description:
Background Illumina
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25 years and 10 months (reg. 1999-08-06).

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Keywords {🔍}

quality, data, read, reads, solexaqa, sequencing, article, figure, information, illumina, software, sequence, dataset, package, tiles, pubmed, genome, bmc, authors, bioinformatics, scores, nucleotide, trimming, assembly, novo, google, scholar, downstream, individual, error, tile, datasets, base, file, trimmed, central, original, illuminas, run, statistics, users, defects, pipeline, dynamic, massey, zealand, cookies, secondgeneration, cox, sequences,

Topics {✒️}

springer nature phred quality score implementation programs high-throughput dna sequencing a-glance quality assessment illumina-style fastq format k-mer parameter sweep application 'usable' information content author information authors user-defined quality threshold 50-bp single-end sequencing high-performance unix machines log-based quality scores solexa/illumina fastq variants tile-based quality control bio-protection research centre user-friendly software package read-level quality data base quality scores background authors scientific editing sequence data quality fastq sequence files idiosyncratic nature privacy choices/manage cookies authors’ original file probabilistic base calling sequence read files downstream applications based base call error incorrectly called base manipulate sequence data species-specific assembly effects a-glance assessment full size image genome analyzer ii quantify data quality proprietary pipeline software tile-specific air bubbles primary unix support reference genome sequence true genome sequence quality scores exceed good quality data quality threshold required haploid reference sequence a-glance graphics give detailed information produce k-mers

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WebPage:
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         headline:SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
         description:Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data. We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.
         datePublished:2010-09-27T00:00:00Z
         dateModified:2010-09-27T00:00:00Z
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ScholarlyArticle:
      headline:SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
      description:Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data. We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.
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         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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      name:The Bio-Protection Research Centre, New Zealand
      name:Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
      name:Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
      name:Massey Genome Service, Massey University, Palmerston North, New Zealand

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