FastQ Screen: A tool for multi-genome mapping and quality control.
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ABSTRACT:
SUBMITTER: Wingett SW
PROVIDER: S-EPMC6124377 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDue to the technological progress in Next Generation Sequencing (NGS), the amount of genomic data that is produced daily has seen a tremendous increase. This increase has shifted the bottleneck of genomic projects from sequencing to computation and specifically storing, managing and analyzing the large amount of NGS data. Compression tools can reduce the physical storage used to save large amount of genomic data as well as the bandwidth used to transfer this data. Recently, DNA sequence compression has gained much attention among researchers.ResultsIn this paper, we study different techniques and algorithms used to compress genomic data. Most of these techniques take advantage of some properties that are unique to DNA sequences in order to improve the compression rate, and usually perform better than general-purpose compressors. By exploring the performance of available algorithms, we produce a powerful compression tool for NGS data called MZPAQ. Results show that MZPAQ outperforms state-of-the-art tools on all benchmark datasets obtained from a recent survey in terms of compression ratio. MZPAQ offers the best compression ratios regardless of the sequencing platform or the size of the data.ConclusionsCurrently, MZPAQ's strength is its higher compression ratio as well as its compatibility with all major sequencing platforms. MZPAQ is more suitable when the size of compressed data is crucial, such as long-term storage and data transfer. More efforts will be made in the future to target other aspects such as compression speed and memory utilization.
| S-EPMC6547476 | biostudies-literature
Project description:BackgroundSome applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling.ResultsFor each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer's bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent.ConclusionMuch more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.
| S-EPMC5374548 | biostudies-literature
Project description:BackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.
| S-EPMC6599294 | biostudies-literature
Project description:FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.
| S-EPMC2847217 | biostudies-literature
Project description:This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled. Precautions must also be undertaken when using long read sequencing technology, which may also lead to misassembled contigs.
| S-EPMC5320493 | biostudies-literature
Project description:SummaryLimitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website.Availabilityhttp://bioinf.spbau.ru/quast .Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC3624806 | biostudies-literature
Project description:In collaboration with the health ministries that we serve and other partners, we set out to complete the multiple-country Global Trachoma Mapping Project. To maximize the accuracy and reliability of its outputs, we needed in-built, practical mechanisms for quality assurance and quality control. This article describes how those mechanisms were created and deployed. Using expert opinion, computer simulation, working groups, field trials, progressively accumulated in-project experience, and external evaluations, we developed 1) criteria for where and where not to undertake population-based prevalence surveys for trachoma; 2) three iterations of a standardized training and certification system for field teams; 3) a customized Android phone-based data collection app; 4) comprehensive support systems; and 5) a secure end-to-end pipeline for data upload, storage, cleaning by objective data managers, analysis, health ministry review and approval, and online display. We are now supporting peer-reviewed publication. Our experience shows that it is possible to quality control and quality assure prevalence surveys in such a way as to maximize comparability of prevalence estimates between countries and permit high-speed, high-fidelity data processing and storage, while protecting the interests of health ministries.
| S-EPMC6159583 | biostudies-literature
Project description:Every laboratory performing mass spectrometry based proteomics strives to generate high quality data. Among the many factors that influence the outcome of any experiment in proteomics is performance of the LC-MS system, which should be monitored continuously. This process is termed quality control (QC). We present an easy to use, rapid tool, which produces a visual, HTML based report that includes the key parameters needed to monitor LC-MS system perfromance. The tool, named RawBeans, can generate a report for individual files, or for a set of samples from a whole experiment. We anticipate it will help proteomics users and experts evaluate raw data quality, independent of data processing. The tool is available here: https://bitbucket.org/incpm/prot-qc/downloads.
2021-03-11 | PXD022816 | Pride
Project description:BackgroundThe German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics.ResultsCAFTAN is built around the mapping of cDNAs to the genome assembly, and the subsequent analysis of their genomic context. It uses sequence features like the presence and type of PolyA signals, inner and flanking repeats, the GC-content, splice site types, etc. All these features are evaluated in individual tests and classify cDNAs according to their sequence quality and likelihood to have been generated from fully processed mRNAs. Additionally, CAFTAN compares the coordinates of mapped cDNAs with the genomic coordinates of reference sets from public available resources (e.g., VEGA, ENSEMBL). This provides detailed information about overlapping exons and the structural classification of cDNAs with respect to the reference set of splice variants. The evaluation of CAFTAN showed that is able to correctly classify more than 85% of 5950 selected "known protein-coding" VEGA cDNAs as high quality multi- or single-exon. It identified as good 80.6 % of the single exon cDNAs and 85 % of the multiple exon cDNAs. The program is written in Perl and in a modular way, allowing the adoption of this strategy to other tasks like EST-annotation, or to extend it by adding new classification rules and new organism databases as they become available. We think that it is a very useful program for the annotation and research of unfinished genomes.ConclusionCAFTAN is a high-throughput sequence analysis tool, which performs a fast and reliable quality prediction of cDNAs. Several thousands of cDNAs can be analyzed in a short time, giving the curator/scientist a first quick overview about the quality and the already existing annotation of a set of cDNAs. It supports the rejection of low quality cDNAs and helps in the selection of likely novel splice variants, and/or completely novel transcripts for new experiments.
| S-EPMC1636072 | biostudies-literature
Project description:This paper provides details on the necessary steps to assess and control data in genome wide association studies (GWAS) using genotype information on a large number of genetic markers for large number of individuals. Due to varied study designs and genotyping platforms between multiple sites/projects as well as potential genotyping errors, it is important to ensure high quality data. Scripts and directions are provided to facilitate others in this process.
| S-EPMC5007749 | biostudies-other