:: DESCRIPTION
Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.
Song L, Florea L.
Gigascience. 2015 Oct 19;4:48. doi: 10.1186/s13742-015-0089-y.
:: DESCRIPTION
Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology.
::DEVELOPER
Department of Genetics / Bioinformatics Group, Max Planck Institute for Evolutionary Anthropology, Leipzig
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.
Improved base calling for the Illumina Genome Analyzer using machine learning strategies.
Kircher M, Stenzel U, Kelso J.
:: DESCRIPTION
BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 May 6. pii: btv290.
BFC: correcting Illumina sequencing errors.
Li H
:: DESCRIPTION
FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.
fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. Fermi-lite is largely a miniature of FermiKit.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.
:: DESCRIPTION
GenomeStudio is a software to visualize and analyze data generated by all of Illumina’s platform.This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome AnalyzerIIx and microarray-based data generated by the iScan System. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results for your genome analysis and research.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2011;784:77-98. doi: 10.1007/978-1-61779-289-2_6.
Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay.
April CS, Fan JB.
:: DESCRIPTION
Alta-Cyclic is a novel Illumina Genome-Analyzer (Solexa) base caller.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Erlich Y, Mitra PP, Delabastide M, McCombie WR & Hannon GJ.
Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.
Nat Methods. 2008 Jul 6.
:: DESCRIPTION
Illuminate parses the metrics binaries that result from Illumina sequencer runs, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, illuminate allows you to print sequencing run metrics to the command line as well as work with the data programmatically.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
dbcAmplicons is a python application for processing massively multiplexed Illumina amplicon runs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.
