• BWA

  • Referenced in 47 articles [sw34374]
  • first algorithm is designed for Illumina sequence reads up to 100bp, while the rest ... than BWA-backtrack for 70-100bp Illumina reads...
  • Soap

  • Referenced in 38 articles [sw08915]
  • parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous...
  • beadarray

  • Referenced in 10 articles [sw06092]
  • control and low-level statistical analysis of Illumina BeadArrays The Illumina BeadArray platform ... illustrate the image processing steps used by Illumina and corresponding methods available in beadarray...
  • PennCNV

  • Referenced in 16 articles [sw19390]
  • kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates...
  • ABySS

  • Referenced in 12 articles [sw17343]
  • African male publicly released by Illumina, Inc. Approximately 2.76 million contigs ≥100 base pairs...
  • IMA

  • Referenced in 5 articles [sw23822]
  • package for high-throughput analysis of Illumina’s 450K Infinium methylation data. The Illumina Infinium ... sites within human genome. Illumina Methylation Analyzer (IMA) is a computational package designed to automate ... microarray. The pipeline loads the data from Illumina platform and provides user-customized functions commonly...
  • SOAPdenovo

  • Referenced in 8 articles [sw17028]
  • program is specially designed to assemble Illumina GA short reads. It creates new opportunities...
  • SHARCGS

  • Referenced in 8 articles [sw29573]
  • genome of Helicobacter acinonychis on the Illumina 1G sequencing instrument and assembled 937 contigs covering...
  • lumi

  • Referenced in 3 articles [sw08431]
  • lumi: a pipeline for processing Illumina microarray. Illumina microarray is becoming a popular microarray platform ... BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies ... Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality ... technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control...
  • Quake

  • Referenced in 5 articles [sw12012]
  • deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts...
  • GRASS

  • Referenced in 5 articles [sw12609]
  • compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes...
  • Trimmomatic

  • Referenced in 5 articles [sw17091]
  • Trimmomatic: a flexible trimmer for Illumina sequence data. Motivation: Although many next-generation sequencing...
  • SCALCE

  • Referenced in 5 articles [sw23321]
  • files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid...
  • GenoSNP

  • Referenced in 4 articles [sw34351]
  • developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely...
  • SolexaQA

  • Referenced in 2 articles [sw17092]
  • SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. Background: Illumina...
  • COHCAP

  • Referenced in 3 articles [sw23514]
  • analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted...
  • Mash

  • Referenced in 3 articles [sw28785]
  • time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data...
  • miRExpress

  • Referenced in 3 articles [sw29587]
  • miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant...
  • SRA

  • Referenced in 3 articles [sw31696]
  • sequencing platforms, including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD System®, Helicos...
  • PEAR

  • Referenced in 3 articles [sw34389]
  • PEAR: a fast and accurate Illumina Paired-End reAd mergeR. PEAR is an ultrafast, memory...