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illumina平台测序原理及常见测序文库构建_生物学_自然科学_专业资料。illumina 平台...上p5接 头相同 文库构建的目的是在目的dna片段两端都连接上想要 的接头 文库.........
illumina高通量测序接头引物_生物学_自然科学_专业资料。illumina高通量测序接头引物列表,评价测序结果质量必备!truseq universal adapter 5’ aatgatacggcgaccaccgagatc.........
illumina 测序原理_生物学_自然科学_专业资料。illumina dna 测序原理 david chen...p5 8oxog-p7 u-p5 single read periodate linearization 单侧测序芯片 一种.........
illumina各测序试剂盒接头序列引物序列信息2015年10月_生物学_自然科学_专业资料。2015年10月的illumina各个测序试剂盒接头序列以及试剂盒引物信息 .........
illumina各测序试剂盒接头序列引物序列信息2014年8月_生物学_自然科学_专业资料。日的illumina各个测序试剂盒接头序列以及试剂盒引物信息 .........
接头和文库接头:与flow cell结合区 read1和read2测序引物结合区 index 用来区分不同样本 3 illumina测序流程 library preparation 文库制备 测序流程 cluster .........
illumina各测序试剂盒接头序列引物序列信息2014年8月_基础医学_医药卫生_专业资料。confidential illumina, inc. 5200 illumina way san diego, ca 92122 u.s.a. .........
diol diol diol flow cell接头 p7 p5 模板杂交 延长 变性 single-read 测序 ...base calls 4 数据分析 拍照图片 intensities reads alignments illumina cbot ?.........
illumina基因测序仪中文测序原理_生物学_自然科学_专业资料。illumina基因测序仪...(~ 6 hrs) 片段化的dna 末端修饰 添加一个a 两端加接头 选择加上接头的 .........
illumina测序前文库制备_基础医学_医药卫生_专业资料...(klenow exo-、dntp) 连接接头 (t4 dna ligase) ...nebnext primer bc = 6-base barcodeindex p5 .........
平台设备 cbot paired-end genome analyzeriix modual 技术原理 illumina 测序技术结合了微阵列技术和专有的可逆终止子技术进行大规模平 行的边合成边测序,通过接头.........
08illumina二代测序分析软件介绍_生物学_自然科学_专业资料。illumina 经典 二代测序原理详解 2016 illumina 用户大会生物信息技术支持 张金丽 .........
day1_01_ts_illumina_sbs二代测序简介-中国区武汉培训_生物学_自然科学_专业资料...一种接头 室温进行反应· ,以维持互补部分序列相互结合的状态 5’ p5 rd1 s.........
illumina测序reads过滤_生物学_自然科学_专业资料。illumina 测序 reads 过滤标准...可能是由于测序荧光强度不够造成; 5) 去除 reads 中含有的接头序列; 6) 去除.........
用 abi 3730 或 roche gs flx titanium 测序, 搭建骨架,再用 illumina solexa...这些捕获的片段再经末 端修饰和加上特定接头后建成 mate-pair 文库,然后上机.........
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暂无评价|0人阅读|0次下载illumina测序_生物学_自然科学_专业资料。创新助手报告 ——主题分析报告 创新助手平台提供 北京.........
本回顾重点介绍了近期利用illumina测序技术来快速追踪天然的、实验室的和临床......
index:标签,在 illumina 平台的多重测序(multiplexed sequencing)过程中会使用 ...(2~5kb) , 加上接头,进行基因簇 cluster 制备或电子扩增 e-pcr,最后.........
illumina 、454 、abi 测序仪比较 illumina 测序仪 illumina 公司的新一代测序...接头也将用于后续的纯化,扩增和测序步骤。 具有 a、b 接头的单链 dna 片段.........
illumina基因测序仪中文测序原理_生物学_自然科学_专业资料。illumina基因测序仪...(~ 6 hrs) 片段化的dna 末端修饰 添加一个a 两端加接头 选择加上接头的 .........
illumina各测序试剂盒接头序列引物序列信息2015年10月_生物学_自然科学_专业资料。2015年10月的illumina各个测序试剂盒接头序列以及试剂盒引物信息 .........
illumina各测序试剂盒接头序列引物序列信息2014年8月_生物学_自然科学_专业资料。日的illumina各个测序试剂盒接头序列以及试剂盒引物信息 .........
illumina高通量测序接头引物_生物学_自然科学_专业资料。illumina高通量测序接头引物列表,评价测序结果质量必备!truseq universal adapter 5’ aatgatacggcgaccaccgagatc.........
–oh 杂交read 1 引物 将测序引物杂交到文库的接头上 read1 测序引 物 illumina 测序流程文库构建(~ 6 hrs) 1-8 samples cbot hiseq2500 miseq 1-8 samples.........
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illumina 测序原理_生物学_自然科学_专业资料。illumina dna......
平台设备 cbot paired-end genome analyzeriix modual 技术原理 illumina 测序技术结合了微阵列技术和专有的可逆终止子技术进行大规模平 行的边合成边测序,通过接头.........
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二代测序数据分析软件包大全
主题帖子积分
　　二代测序数据预处理与分析
　　使用的工具列表
　　· 质量控制Quality Control：FastQC、Fastx-toolkit· 拼接Aligner：BWA，Bowtie, Tophat, SOAP2· Mapper：Tophat, Cufflinks· 基因定量 Gene Quantification: Cufflinks, Avadis NGS· 质量改进 Quality improvement: Genome Analysis Toolkit(GATK)· SNP: Unified Genotyper,Glfmultiple, SAMtools, Avadis NGS· CNV: CNVnator· Indel: Pindel, Dindel, Unified Genotyper, Avadis NGS· Mapping to a gene: Cufflinks, Rsamtools, Genomic Features
　　数据处理的流程
　　2. 基于新一代测序技术的综合分析软件NextGENe，提供序列组装、定位、变异、查找、表达差异分析等全套解决方案
　　英文介绍：/NextGENe.html
　　中文介绍：.cn/a/products/biotechnology/.html
　　引用文章列表：/conference.html#ng
　　用户列表：/userlistNG.html
　　2. 基于新一代测序技术的综合分析软件NextGENe，提供序列组装、定位、变异、查找、表达差异分析等全套解决方案
　　英文介绍：/NextGENe.html
　　中文介绍：.cn/a/products/biotechnology/.html
　　引用文章列表：/conference.html#ng
　　用户列表：/userlistNG.html
　　二代测序数据分析：[1]quality control
　　从事生物信息学分析的学生和工作人员都会接触到二代测序数据，我们从测序公司拿到所需要的数据之后，首先最关心的问题就是测序数据的质量好不好，本文介绍一下如何对二代测序数据进行质量分析(QC)
　　工具/原料linux系统：ubuntu 或者 服务fastqc
　　方法/步骤
　　1. 安装fastqc注意将fastqc加入到系统环境变量中，以便于在终端或命令行中直接运行具体安装方法参考fastqc官方手册
　　2. 在命令行中直接运行命令fastqc [-o output dir]
　　[--(no)extract]
　　[-f fastq]
　　[-c contaminant file]output dir指的是输出结果路径extract参数指的是输出结果是否解压-f 参数 是输入文件的格式，指的是测序数据
　　3 运行fastqc： fastqc seqfile1.fq seqfile2.fq
getimg.php?url=http%3A%2F%2Fmmbiz.qpic.jpg (5.11 KB, 下载次数: 0)
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　　4. 输出结果：在output dir目录下的一个压缩文件(未压缩)通常我们只需关注如下几个结果：a）每个位置的碱基测序质量。通常我们一般认为从第二个碱基开始，平均每个碱基的测序质量boxplot下四分位线在30分以上，则认为测序质量非常好
　　B）每条序列的测序质量 一般认为90%的reads测序质量在35分以上，则认为该测序质量非常好
　　C）ATCG碱基在各个位置上的分布 一般来说，AT含量高于CG含量，AT含量约28%，CG含量约22%。由于测序问题，通常第一二位置的碱基测序质量比较低，ATCG含量也不正常。这种情况不影响数据质量，如果实在介意，可在后续bowtie mapping的时候将前两个碱基去掉。
　　Integrated solutions
　　*CLCbio Genomics Workbench-de novoand reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux.
　　*Galaxy- Galaxy = interactive and reproducible genomics. A job webportal.
　　*Genomatix- Integrated Solutions for Next Generation Sequencing data analysis.
　　*JMP Genomics- Next gen visualization and statistics tool from SAS. They areworking with NCGRto refine this tool and produce others.
　　*NextGENe-de novoand reference assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via anchors into mini-contigs before assembly. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Win or MacOS.
　　* SeqMan Genome Analyser- Software for Next Generation sequence assembly of Illumina, Roche FLX and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Commercial. Win or Mac OS X.
　　*SHORE- SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. A suite created by the 1001 Genomes project. Source for POSIX.
　　*SlimSearch- Fledgling commercial product.
　　Align/Assemble to a reference
　　*BFAST- Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.
　　*Bowtie- Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index.Link to discussion thread here. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.
　　*BWA- Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source.
　　*ELAND- Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.
　　*Exonerate- Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
　　*GenomeMapper- GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX.
　　*GMAP- GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.
　　*gnumap- The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix.
　　*MAQ- Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source
　　*MOSAIK- MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Str?mberg at Boston College. Win/Linux/MacOSX
　　*MrFAST and MrsFAST- mrFAST&&mrsFAST are designed to map short reads generated with the Illumina platform to referen in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source.
　　*MUMmer- MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.
　　*Novocraft- Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.
　　*PASS- It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.
　　*RMAP- Assembles 20 - 64 bp Illumina reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.
　　*SeqMap- Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.
　　*SHRiMP- Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX.
　　*Slider- An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper ishere.
　　*SOAP- SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX.
　　*SSAHA- SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha.
　　*SOCS- Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH.
　　*SWIFT- The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM)
　　*SXOligoSearch- SXOligoSearch is a commercial platform offered by the Malaysian basedSynamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.
　　*Vmatch- A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX.
　　*Zoom- ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data.
　　De novoAlign/Assemble
　　*ABySS- Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. By Simpson JT and others at the Canada's Michael Smith Genome Sciences Centre. C++ as source.
　　*ALLPATHS- ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Broad Institute.
　　*Edena- Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hernandez, P. Fran?ois, L. Farinelli, M. Osteras, and J. Schrenzel. Linux/Win.
　　*EULER-SR- Short readde novoassembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach.
　　*MIRA2- MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
　　*SEQAN- A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads. By Tobias Rausch and others. C++, Linux/Win.
　　*SHARCGS- De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
　　*SSAKE- The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
　　*SOAPdenovo- Part of the SOAP suite. See above.
　　*VCAKE- De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
　　*Velvet- Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
　　SNP/Indel Discovery
　　*ssahaSNP- ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
　　*PolyBayesShort- A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.
　　*PyroBayes- PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College.
　　Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database
　　*EagleView- An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
　　*LookSeq- LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, low or high- and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre.
　　*MapView- MapView: visualization of short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. Linux.
　　*SAM- Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux.
　　*STADEN- Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is availablehere
　　*XMatchView- A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.
　　Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq
　　*BS-Seq- The source code and data for the Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning Nature paper byCokus et al.(Steve Jacobsen's lab at UCLA). POSIX.
　　*CHiPSeq- Program used by Johnson et al. (2007) in their Science publication
　　*CNV-Seq- CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Chao Xie and Martti T Tammi at the National University of Singapore. Perl/R.
　　*FindPeaks- perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of theVancouver Short Read Analysis Package
　　*MACS- Model-based Analysis for ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab.
　　*PeakSeq- PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls. a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. By Rozowsky J et al. C/Perl.
　　*QuEST- Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publicationGenome-wide analysis of transcription factor binding sites based on ChIP-Seq data. (C++)
　　*SISSRs- Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl.
　　*See alsothis threadfor ChIP-Seq, until I get time to update this list.
　　Alternate Base Calling
　　*Rolexa- R-based framework for base calling of Solexa data. Projectpublication
　　*Alta-cyclic- a novel Illumina Genome-Analyzer (Solexa) base caller
　　Transcriptomics
　　*ERANGE- Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Supports Bowtie, BLAT and ELAND. From the Wold lab.
　　*G-Mo.R-Se- G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads. From CNS in France.
　　*MapNext- MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.
　　*QPalma- Optimal Spliced Alignments of Short Sequence Reads. Authors are Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar R?tsch. A paper isavailable.
　　*RSAT- RSAT: RNA-Seq Analysis Tools. RNASAT is developed and maintained by Hui Jiang at Stanford University.
　　*TopHat- TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland and the University of California, Berkeley
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