Tag Archives: NGS

七 14

讨论-用高通量测序方法研究sepsis

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估计很多小伙伴都没有听过sepsis，现在翻译成中文是脓毒病，很多人会把它与那个缺乏维他命C的败血症混淆，其实完全不一样，因为sepsis致死率非常高！

sepsis 英[ˈsepsɪs] 美['sepsɪs]
n. 脓毒病; 脓毒疾;
[例句]This may be of value in the treatment of meningitis and sepsis.
这可能会在治疗脑膜炎和败血症上有一定价值。

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十 16

NGS数据比对工具持续收集

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无意中看到了这个网站，比wiki的还有全面和专业。搜集了现有还算比较出名的比对软件，并且列出来了，还做了简单评价，里面对比对工具的收集，主要是基于2012年的一个综述《Tools for mapping high-throughput sequencing data》，相信应该是有不少人都看过这篇综述的，其实生物信息初学者应该自己去文献数据库找点感兴趣的关键词的综述多看看，广泛涉猎总没有坏处的。

<img src="http://www.ebi.ac.uk/~nf/hts_mappers/mappers_timeline.jpeg" alt="Mappers Timeline" width="800">

Features Comparison

The following Table enables a comparison of mappers based on different characteristics. The table can be sorted by column (just click on the column name). The data was collected from different sources and in some cases was provided by the developers. For execution times and memory requirements we refer to the above mentioned review (supplementary data is available here).

The Data column indicates if the mapper is specifically tailored for DNA, RNA, miRNA, or bisulfite sequences.The Seq.Plat. column indicates if the mapper supports natively reads from a specific sequencing platform or not (N). The version column indicates the version of the mapper considered. Read length limits are showed in two columns: minimum read length (Min. RL) and maximum read length (Max. RL.). Unless otherwise stated the unit is base pairs. The support for mismatches and short indels is also presented including, when possible, the maximum number of allowed mismatches and indels: by default the value is presented in bases; in some cases the value is presented as a percentage of the read size; or as score, meaning that mapper uses a score function. The alignments reported column indicate the alignments reported when a read maps to multiple locations. The alignment column indicates if the reads are aligned end-to-end (Globally) or not (Locally). The Parallel column indicates if the mapper can be run in parallel and, if yes, how: using a shared-memory (SM) or/and a distributed memory (DM) computer. The QA (quality awareness) column indicates if the mapper uses read quality information during the mapping. The support for paired-end/mate-pair reads is indicated in the PE column. The Splicing column indicates, for the RNA mappers, if the detection of splice junctions is made de novo or/and through user provided libraries (Lib). The Index column indicates if the reads or/and the reference are indexed. The number of citations was obtained from Google Scholar on 13 June 2015.
三 29

NGS QC Toolkit 对测序reads进行简单过滤

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这个软件其实我真心不需要讲些什么了，它的官网写的太好了，简直就是软件说明书的典范

http://www.nipgr.res.in/ngsqctoolkit.html

它列出了它的几个功能模块，还给出了下载地址，还给出了说明文档，下载压缩包，解压即可使用啦

更重要的是给出了测试数据和测试的结果，而且还专门测试了不同测序平台及不同的测序策略的使用说明

 

NGS QC Toolkit 对测序reads进行简单过滤264

里面就是一些perl测序，其实自己都可以写的，分成了四大类。

其中统计的那个平均测序质量，我在前面仿写fastqc就写过，至于那个统计N50，更是生信常用的脚本。

但是大家可以看看这个perl程序来学perl语言，蛮不错的这些程序，都写的很标准。

比如那个TrimmingReads.pl

NGS QC Toolkit 对测序reads进行简单过滤576

可以根据四个参数来选择性的对我们的原始reads进行过滤，当然很多其它的程序也有类似的功能，它的参数分别是铲掉5端的几个碱基或者3端的，或者根据测序质量来切除碱基，或者根据reads长度来取舍，都是挺实用的功能。但是我一般用LengthSort和DynamicTrim那两个程序，原因很简单，我老师是这样用的，所以我习惯了，哈哈