2019-07-29 Alignment-free RNA qu

2019-07-29 本文已影响0人阿乜太帅

主要介绍跳过比对直接进行定量的三个软件的资料链接及比较 (Alignment-free RNA quantification)

总结：软件性能上：salmon >= kallisto > sailfish ， kallisto务必使用最新版，老版本有巨大bug

Q: Alignment-free RNA quantification？

A: 核心思想是将转录本划分成kmer, 以kmer出现的次数作为转录本丰度的衡量证据。当然实际处理时，会非常的复杂。因为同一个kmer会对应多个转录本，一个转录本会出现相同的kmer等情况，kmer的次数如何合理分配就很关键

文献：

Alignment-free sequence comparison: benefits, applications, and tools
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1319-7
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1. sailfish

Sailfish: Rapid Alignment-free Quantification of Isoform Abundance

1.1. 官方网址：

http://www.cs.cmu.edu/~ckingsf/software/sailfish/index.html
Overview：RNA-seq expression estimates need not take longer than a cup of coffee

1.2. 文献：

Rob Patro, Stephen M. Mount, and Carl Kingsford (2014) Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology (doi:10.1038/nbt.2862)

1.3. 相关博文：

sailfish:不需要比对的转录本定量软件（生信修炼手册）https://mp.weixin.qq.com/s/oGn_3AqR-jazap0zYobhvg

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2. salmon

salmon —Don't count . . . quantify!

2.1. 官方网址：

https://combine-lab.github.io/salmon/
Overview：Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.

2.2. 文献：

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.

2.3. 相关博文：

salmon: sailfish的升级版本生信修炼手册 https://mp.weixin.qq.com/s/6C28Sv5HdTSKKFm0mn9l1g

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3. kallisto

3.1. 官方网址：

https://pachterlab.github.io/kallisto/
Overview：kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

3.2. 文献：

Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519

3.3. 相关博文：

精品RNA分析软件| kallisto，卡丽丝多（生信草堂）https://mp.weixin.qq.com/s/MyESabzuI1F2X-rZn1L3UA

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4. 比较

4.1. 转录组分析工具大比拼

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (Nature Communications DOI: 10.1038/s41467-017-00050-4)
翻译参考:（生信宝典） https://mp.weixin.qq.com/s/xAaj-d5LRRj0SSMFJ7Yo9Q

4.2. 39个RNAseq分析工具与对比

Sahraeian S M E, Mohiyuddin M, Sebra R, et al. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis[J]. Nature Communications, 2017, 8(1):59.
博文参考：（生信人） https://mp.weixin.qq.com/s/mnYV7T_2Ut1xRavGv1nv5g

4.3. 评估salmon和kallisto在小麦RNA-seq定量中的异同

（小麦研究联盟） https://mp.weixin.qq.com/s/vdACPZJ-cUfU_jJG6WJakA