It is particular designed for 454/Roche data, but can also be used for other types of sequence.
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PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data.It also includes few other tools, which are helpful in NGS data quality control and analysis. The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. NGS QC Toolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data.NGSQC: cross-platform quality analysis pipeline for deep sequencing data.MultiQC - Aggregate and visualise results from numerous tools (FastQC, HTSeq, RSeQC, Tophat, STAR, others.) across all samples into a single report.mRIN - Assessing mRNA integrity directly from RNA-Seq data.
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FastQC can be run as a stand-alone application or it can be integrated into a larger pipeline solution. Results are presented in HTML permanent reports. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Import of data is possible from FastQ files, BAM or SAM format.
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Some important questions like sequencing depth/coverage or how many biological or technical replicates must be carefully considered.
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