SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

A reference human genome dataset of the BGISEQ-500 sequencer

(2017) Jie Huang et al.   GigaScience

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

(2016) Marc Sturm et al.   BMC BIOINFORMATICS

The cytoskeleton adaptor protein ankyrin-1 is upregulated by p53 following DNA damage and alters cell migration

(2016) A E Hall et al.   Cell Death & Disease

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm

(2015) Yun-Lung Li et al.   BMC BIOINFORMATICS

Optimization of miRNA-seq data preprocessing

(2015) S. Tam et al.   BRIEFINGS IN BIOINFORMATICS

A highly specific microRNA-mediated mechanism silences LTR retrotransposons of strawberry

(2015) Nada Šurbanovski et al.   PLANT JOURNAL

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Prevention, diagnosis and treatment of high-throughput sequencing data pathologies

(2014) Xiaofan Zhou et al.   MOLECULAR ECOLOGY

Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data

(2014) Qian Zhou et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

Three-stage quality control strategies for DNA re-sequencing data

(2013) Y. Guo et al.   BRIEFINGS IN BIOINFORMATICS

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

High-throughput sequencing for biology and medicine

(2013) W. W. Soon et al.   Molecular Systems Biology

Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

(2013) Xiujun Zhang et al.   PLoS One

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

The Suppression of WRKY44 by GIGANTEA-miR172 Pathway Is Involved in Drought Response of Arabidopsis thaliana

(2013) Yingying Han et al.   PLoS One

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

(2012) Tongwu Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma

(2011) Liang Zhou et al.   PLoS One

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS