转录组分析常用软件汇总--精华版
一、比对工具
(Kim et al., 2015) HISAT: a fast spliced aligner with low memory requirements. Nature methods.
Aligns RNA-q reads to a reference genome using uncompresd suffix arrays. STAR has a potential for accurately aligning long (veral kilobas) reads that are emerging from the third-generation quencing technologies.
掩耳盗铃什么意思(Dobin et al., 2013) STAR: ultrafast universal RNA-q aligner. Bioinformatics.
Self-training Algorithm for Splice Junction Detection using RNA-q.
(Li et al., 2013) TrueSight: a new algorithm for splice junction detection using RNA-q. Nucleic acids rearch.
A toolkit for processing next-gen quencing data. The programs were also implemented
in Bioconductor R package Rsubread.
(Liao et al., 2013) The Subread aligner吸血乌贼: fast, accurate and scalable read mapping by ed-and-vote. Nucleic acids rearch.
(Rogers et al., 2012) SpliceGrapher公推直选: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome biology.
(Philippe et al., 2013) CRAC新学期新征程内容: an integrated approach to the analysis of RNA-q reads. Genome biology.
A fast splice junction mapper for RNA-Seq reads. TopHat aligns RNA-Seq reads to mammalian-sized genomes using the high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
(Kim et al., 2013) TopHat2: accurate alignment of transcriptomes in the prence of inrtions, deletions and gene fusions. Genome Biol.
(Chu et al., 2015) SpliceJumper: a classification-bad approach for calling splicing junctions from RNA-q data. BMC bioinformatics.
(Srivastava et al., 2016) RapMap: a rapid, nsitive and accurate tool for mapping RNA-q reads to transcriptomes. Bioinformatics.
A framework for genome-bad transcript reconstruction and quantification. CIDANE is engineered to not only asmbly RNA-q reads ab initio, but to also make u of the growing annotation of known splice sites, transcription start and end sites, or even full-length transcripts, available for most model organisms. To some extent, CIDANE is able to recover splice junctions that are invisible to existing bioinformatics tools.
(Canzar et al., 2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome biology.
蕊寒香冷An open source tool for accurate genome-guided transcriptome asmbly from RNA-q reads bad on the model of splice graph. An extension of our program CLASS, CLASS2
jointly optimizes read patterns and the number of supporting reads to score and prioritize transcripts, implemented in a novel, scalable and efficient dynamic programming algorithm.
(Song et al., 2016) CLASS2: accurate and efficient splice variant annotation from RNA-q reads. Nucleic acids rearch.
二、Read数统计
An RNA-q read counting tool which builds upon the speed of featureCounts and implements the counting modes of HTSeq. VERSE is more than 30x faster than HTSeq when computing the same gene counts. VERSE also supports a hierarchical assignment scheme, which allows reads to be assigned uniquely and quentially to different types of features according to ur-defined priorities. It is built on top of featureCounts.
(Zhu et al., 2016) VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv.
海龟英文A tool for RNA-Seq data analysis that counts for each gene how many aligned reads over夏天的夜
lap its exons.
(Anders et al., 2013) Count-bad differential expression analysis of RNA quencing data using R and Bioconductor. Nature protocols.
A package that provides efficient low-level and highly reusable S4 class for storing ranges of integers, RLE vectors (Run-Length Encoding) and, more generally, data that can be organized quentially (formally defined as Vector objects), as well as views on the Vector objects. IRanges provides also efficient list-like class for storing big collections of instances of the basic class. All class in the package u consistent naming and share the same rich and consistent 'Vector API' as much as possible.远人
(Lawrence et al., 2013) Software for computing and annotating genomic ranges. PLoS computational biology.
A read summarization program, which counts mapped reads for the genomic features such as genes and exons.
(Liao et., 2013) featureCounts: an efficient general-purpo program for assigning quence reads to genomic features. Bioinformatics
