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 Some splice junction detecting tools based on RNA-Seq data
  TopHat
TopHat is a fast splice junction mapper for RNA-Seq reads. From Center for Bioinformatics and Computational Biology at University of Maryland.
  SpliceMap
SpliceMap is a de novo splice junction discovery tool. Developed by Wong Lab at Stanford university.
  Supersplat
Superplat is an application for discovery of potential splice junctions given HTS data.
  ERANGE
ERANGE is a tool which can be used for both ChIP-Seq and RNA-Seq analyses.
  QPALMA
QPalma is an alignment tool targeted to align spliced reads.
  SplitSeek
SplitSeek is a program for de novo prediction of splice junctions in RNA-Seq data. Developed by Rudbeck Laboratory at Uppsala University.
MapNext
MapNext is a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. Developed by Evolution Genomicsc Lab of SUN YAT-SEN UNIVERSITY.
HMMSplicer
MMSplicer is an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. Developed by DeRisi Lab at University of California, San Francisco.
 Some visualization tools based on next generation sequencing data
EagleView
EagleView is an information-rich genome assembler viewer. It can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
BamView
An easy Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence based on BAM file.
LookSeq
LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. From the Sanger Centre.
SAM
SAM is a application for Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developed at Canada's Michael Smith Genome Sciences Centre.
XMatchView
A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre.
NGSView
NGSView is an extensible open source sequence editor to allow for visualization and manipulation of massive amount of sequence data. From RIKEN Omics Science Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Japan.
IGV
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. Developed at Broad Institute.
MapView
MapView is a visualization tool for short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.
SeqMonk
SeqMonk is a tool to visualise and analyse high throughput mapped sequence data. Developed at the Babraham Institute.
Savant
Savant is a genome browser which combines visualization of HTS and other genome-based data with powerful analytic tools. Developed by Computational Biology Lab at University of Toronto.
Gambit
Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis. Developed by The Marth Lab at Boston College.
inGAP
An integrated next-generation genome analysis pipeline to detect single nucleotide polymorphisms (SNPs) and insertion/deletions (indels).
MagicViewer
MagicViewer is developed to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. From Institute of Genomic Medicine at Wenzhou Medical College.
 Some short reads mapping tools
MAQ
Mapping and Assembly with Qualities (renamed from MAPASS2). Written by Heng Li from the Sanger Centre.
BWA
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, and is a progression from MAQ.
Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner. Written by Ben Langmead and Cole Trapnell at University of Maryland .
SOAP
SOAP (Short Oligonucleotide Alignment Program) is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. SOAP2 is an updated program based on Burrows-Wheeler Transform. Developed by Beijing Genomics Institute.
BFAST
BFAST is a Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.
MOSAIK
MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Written by Michael Strömberg at Boston College.
MrFAST and MrsFAST
mrFAST & mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. From Eichler Lab at University of Washington.
Numbers of collected useful next-generation data analysis software can be accessed from SEQanswers wiki

 

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