:: DESCRIPTION
CI Convert converts Leica LIF/XLEF files to Aperio ImageScope SVS/BigTiff and Image Files to Leica LIF (using Bio-Formats).
::DEVELOPER
the Cellular Imaging Core Facility
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SVS (SNP & Variation Suite) is an integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. SVS was created specifically to empower biologists and other researchers to easily perform complex analyses and visualizations, eliminating the need to rely exclusively on bioinformatics experts or cobble together difficult to use, incompatible freeware. With SVS you can focus on your research instead of learning to be a programmer or waiting in line for bioinformaticians.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.
::DEVELOPER
Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jianmin Wang et al.
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods 8, 652–654 (2011)
:: DESCRIPTION
SVMerge is a software to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. SVMerge is modular and extensible allowing new callers to be incorporated as they become available.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wong K, Keane TM, Stalker J, Adams DJ (2010)
SVMerge: Enhanced structural variant and breakpoint detection by integration of multiple detection methods and local assembly,
Genome Biology, 11:R128
:: DESCRIPTION
Breakpointer is a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing (NGS). By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such break-points can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1.
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.
:: DESCRIPTION
PEMer (Paired-End Mapper) is a computational and simulation framework for discovering SVs by paired-end read mapping.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Biol. 2009 Feb 23;10(2):R23.
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.
:: DESCRIPTION
AGE (Alignment with Gap Excision) is a tools that implements an algorithm for optimal alignment of sequences with SVs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Mar 1;27(5):595-603. Epub 2011 Jan 13.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Abyzov A, Gerstein M.
