SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
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Summary
SOAPnuke is demonstrated as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework that enables large scalability to distribute all the processing works to an entire compute cluster.
- Type
- article
- Published
- 2017-12-04
- Cited by
- 1,971
- References
- 52
- Access
- Open access
- OpenAlex
- https://openalex.org/W2774072836
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:24376266
Keywords
Computer science, Scalability, Workflow, Preprocessor, Executable
References
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- The Suppression of WRKY44 by GIGANTEA-miR172 Pathway Is Involved in Drought Response of Arabidopsis thaliana
- SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
- HTQC: a fast quality control toolkit for Illumina sequencing data
- Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma
- Three-stage quality control strategies for DNA re-sequencing data
- AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
- BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data
- Cutadapt removes adapter sequences from high-throughput sequencing reads
- Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis
- Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
- SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
- Prevention, diagnosis and treatment of high‐throughput sequencing data pathologies
- Big Data: Astronomical or Genomical?
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- fastp: an ultra-fast all-in-one FASTQ preprocessor
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- Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan
- Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis
- Fern genomes elucidate land plant evolution and cyanobacterial symbioses
- Heterogeneous and Flexible Transmission of mcr-1 in Hospital-Associated Escherichia coli
- Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize
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- Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
- Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)
- Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
- Polyploid plants have faster rates of multivariate climatic niche evolution than their diploid relatives
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