机器学习和生物信息学实验室联盟

标题: [转载]测序数据分析工具 [打印本页]

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作者: zouquan    时间: 2012-4-28 15:41
标题: [转载]测序数据分析工具
Alignment与mapping:
BLAT: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
CABOG: http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
CLUSTALW: http://www.ebi.ac.uk/Tools/msa/clustalw2
LAGAN & Shuffle-LAGAN: http://lagan.stanford.edu/lagan_web/index.shtml
MUGSY:
http://mugsy.sourceforge.net
MUMmer: http://mummer.sourceforge.net
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Programhttp://research-pub.gene.com/gmap/

Assembly:

SOAPdenovo:
http://soap.genomics.org.cn/soapdenovo.html
Abyss 1.3.0: http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.0
Arachne & AllPath: https://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-
TotalReCaller: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller
Velvet: http://www.ebi.ac.uk/~zerbino/velvet
VISTA tools，包括AVID: http://pipeline.lbl.gov/run5details.shtml
ABI数据分析软件：http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/ngs-data-analysis-software.html
Illumina的软件：http://www.illumina.com/software.ilmn
ION PGM测序仪的社区：http://www.iontorrent.com/forum/

另外附上一些精选的数据分析工具：

名称	链接	评论
基因组重测序
Bwa	http://bio-bwa.sourceforge.net	比对工具
Dindel	http://sites.google.com/site/keesalbers/soft/dindel	小的插入/缺失发现
Erds	http://www.duke.edu/~mz34/erds.htm	拷贝数变异发现
Pindel	http://www.ebi.ac.uk/~kye/pindel/	小的插入/缺失发现
Samtools	http://samtools.sourceforge.net	操控比对后数据的工具
Sequence Variant Analyzer	http://www.svaproject.org	在基因组背景下显示变异
Chip-Seq
Findpeaks	http://vancouvershortr.sourceforge.net
RNA-Seq
Cufflinks	http://cufflinks.cbcb.umd.edu	测定转录本丰度
Tophat	http://tophat.cbcb.umd.edu	剪接点定位
De Novo 拼接
Oases	http://www.ebi.ac.uk/~zerbino/oases/	根据转录组数据拼接
基因组浏览器
Integrated Genome Browser	http://www.bioviz.org/igb/
Integrative Genomics Viewer	http://www.broadinstitute.org/software/igv/

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