• Soap

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

  • Referenced in 3 articles [sw08431]
  • popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different ... from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique ... Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality...
  • beadarray

  • Referenced in 10 articles [sw06092]
  • Illumina BeadArrays The Illumina BeadArray platform is a novel microarray technology based on randomly assembled ... data available. A major advantage of BeadArray technology is the high degree of replication ... illustrate the image processing steps used by Illumina and corresponding methods available in beadarray...
  • TileQC

  • Referenced in 1 article [sw23482]
  • BACKGROUND: Next-generation DNA sequencing technologies such as Illumina’s Solexa platform and Roche...
  • VNTRseek

  • Referenced in 1 article [sw16919]
  • Khoisan genomes (454 technology) and two 1000 Genomes family trios (Illumina). In the Watson genome...
  • GemSIM

  • Referenced in 1 article [sw34550]
  • sequencing technology compatible with the generic formats SAM and FASTQ (including Illumina and Roche/454). GemSIM ... realistically emulate individual sequencing runs and/or technologies. Empirical fragment length and quality score distributions...
  • SHARCGS

  • Referenced in 8 articles [sw29573]
  • cost. Applications of such technologies seem to be limited to resequencing and transcript discovery ... genome of Helicobacter acinonychis on the Illumina 1G sequencing instrument and assembled 937 contigs covering ... suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with...
  • pRESTO

  • Referenced in 2 articles [sw23143]
  • single- or paired-end reads and emerging technologies that use single-molecule identifiers. pRESTO ... tested on data generated from Roche and Illumina platforms. It has a built-in capacity...
  • MIRA

  • Referenced in 1 article [sw02392]
  • GS20, FLX or Titanium); Ion Torrent; Solexa (Illumina) sequencing; (in development) Pacific Biosciences sequencing into ... sequences of different sequencing technologies either in a single assembly run (a true hybrid assembly...
  • GRASS

  • Referenced in 5 articles [sw12609]
  • second-generation high-throughput sequencing (HTS) technologies has sparked a growing interest in de novo ... compared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes...
  • BING

  • Referenced in 1 article [sw29571]
  • data. When compared to the Illumina informatics tool, BING’s pixel-based approach produces ... increasing the density and throughput of NGS technologies...
  • BayesCall

  • Referenced in 1 article [sw29570]
  • main challenges associated with this technology include reducing the error rate, assigning accurate base-specific ... calling algorithm, BayesCall, is introduced for the Illumina sequencing platform. Being founded on the tools...
  • Decombinator

  • Referenced in 1 article [sw23150]
  • quantity of raw data produced by this technology requires efficient ways to categorize and store ... application of finite-state automaton to map Illumina short-read sequence data for individual TcRs...
  • Pilon

  • Referenced in 1 article [sw29702]
  • genome assembly improvement. Advances in modern sequencing technologies allow us to generate sufficient data ... supplied with paired end data from two Illumina libraries with small...
  • R

  • Referenced in 9832 articles [sw00771]
  • R is a language and environment for statistical...
  • GATK

  • Referenced in 17 articles [sw12019]
  • The genome analysis toolkit: a MapReduce framework for...
  • KEGG

  • Referenced in 275 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...
  • Samtools

  • Referenced in 22 articles [sw14583]
  • Samtools is a suite of programs for interacting...
  • FastQC

  • Referenced in 8 articles [sw16946]
  • FastQC: A quality control tool for high throughput...
  • Trimmomatic

  • Referenced in 6 articles [sw17091]
  • Trimmomatic: a flexible trimmer for Illumina sequence data...