The common tools used in the NGS analysis

1. Mapping

  • BFAST: A fast and accurate tool for mapping of short reads to reference sequences.

  • BWA: A fast light-weighted tool that aligns short nucleotide sequences to a sequence database.

  • Bowtie: An ultrafast, memory-efficient short read aligner.

  • ELAND: A very fast alignment algorithms from Illumina company.

  • MAQ: A software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.

  • SHRiMP: A software package for aligning genomic reads against a target genome.

  • SOAP: A tool package that provides full solution to next generation sequencing data analysis (including a alignment tool SOAPaligner/soap2 etc).

  • SOLiD bioscope: A software package that is designed specifically to optimize the accuracy of the ABI SOLiD colorspace data.

  • SWIFT: A software collection for fast index-based sequence comparison.

  • TopHat: A spliced read mapper for RNA-Seq.

2. SNV Detection

  • CASAVA: The internal assembler and variant caller Illumina company utilized.

  • GATK: A multiple-sample, technology-aware SNV and indel caller.

  • JointSNVMix: A probabilistic model for detection of somatic mutations in normal/tumour pair.

  • SAMtools: A set of utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer.

  • SNVMix: A tool for SNV calling based on probabilistic binomial mixture model.

  • SOAPsnp: A tool for identifying SNVs by Beijing Genomics Institute (BGI).

  • Strelka: A tool for somatic small-variant calling from sequenced tumor-normal sample pairs.

  • SomaticSniper: A program to identify SNVs that are different between tumor and normal sample.

  • VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.

3. Indel Detection

  • Dindel: A program for calling small indels from short-read sequence data from Illumina platform.

  • Pindel: A tool for identifying indels and structural variants at single-based resolution from next-generation sequence data.

  • SplazerS: A tool for detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing.

4. Structural Variation Detection

  • BreakDancer: A tool for detecting five types of SVs (insertions, deletions, inversions, inter- and intra-chromosomal translocations) from next generation paired-end sequencing reads.

  • CREST: A software that uses the soft-clipped reads to directly map the breakpoints of SVs.
  • GASV: A tool for identifying and comparing structural variants by computing intersections of breakpoint regions.

  • HYDRA: A tool for detecting structural variants in both unique and duplicated genomic regions.

  • PEMer: A software package for detecting SVs from paired-end reads.

  • R453Plus1Toolbox: An R/Bioconductor package for the analysis of Roche 454 sequencing data.

  • SVMerge: A tool for SVs analysis by integrating calls from several existing SV callers.

  • SVDetect: A tool for identifying structural variations from paired-end/mate pair data.

  • VariationHunter: An tool for identifying structural variations from paired-end WGS data.

5. Copy Number Variation Detection

  • CBS: An R package for detecting CNVs using sequencing data.

  • CMDS: A population-based method for recurrent CNVs analysis from multiple samples.

  • CNAseg: A tool for Identifying CNVs in cancer from NGS data.

  • cnvHMM: A tool for CNVs analysis using Hidden Markov algorithm.

  • CNVnator: A tool for CNV discovery and genotyping from depth of read mapping.

  • FREEC: A tool for control-free CNVs detection using deep-sequencing data.

  • RDXplorer: A tool for CNVs detection in whole human genome sequence data using read depth coverage.

  • SegSeq: A tool for detecting CNVs from short sequence reads.

  • VarScan: A platform-independent, technology-independent software tool for identifying SNVs, indels, and CNVs in massively parallel sequencing of individual and pooled samples.

6. Annotation

  • ANNOVAR: An efficient software tool to use update-to-date information to functionally annotate genetic variants detected from diverse genomes.

  • BreakSeq: A pipeline for annotation, classification and analysis of SVs at single nucleotide resolution.

  • Seattle Seq: An server that provides annotation of SNVs.

7. Data Visualization

  • Avadis: A software for visualizing and analyzing RNA-Seq data.

  • CIRCOS: A software package for visualizing genomic events.

  • IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.

  • Pairoscope: A software package for generating diagrams indicating the relationship of paired end sequencing reads, is most useful for visualizing translocations.

  • UCSC Genome Browser: A genome browser that provide precise access to sequence and annotation data for any genomic region of specific interest.

8. Fusion Gene Detection

  • Avadis: A software for visualizing and analyzing RNA-Seq data.

  • CIRCOS: A software package for visualizing genomic events.

  • IGV: A high-performance visualization tool for interactive exploration of next-generation sequencing data.

  • Pairoscope: A software package for generating diagrams indicating the relationship of paired end sequencing reads, is most useful for visualizing translocations.

  • UCSC Genome Browser: A genome browser that provide precise access to sequence and annotation data for any genomic region of specific interest.

图片处理(PS:Photoshop)

1. 蒙版:通过添加蒙版,实现无损对图片进行操作。图片本身不会受损,所有操作都发生在蒙版上,但是效果跟直接操作图片相同。

2.快捷键

1. shift+拖动:成比例放大、缩小;
2. ctrl+alt+z:持续撤回
3.

3.功能

1. 橡皮擦:
a. 擦到透明
b. 自动锁定边界擦除

2. 吸管+画笔:
用图片中的颜色盖掉图片中的部分,可以显得最自然。

3.

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Syzygy

subtitle: SNP and indel calling for pooled and individual targeted resequencing studies.
link: http://software.broadinstitute.org/software/syzygy/
Institution: broadinstitute

Syzygy is a tool used to call variants in pooled targeted sequencing data. The pooled targeted sequencing experimental design is different in that the reads do no have the identity of the individual it was intended to come from. The pooled targeted sequencing experiment is intened to minimize cost and maximize the utility of the billions of DNA sequence data that is generated by one lane of sequencing run.