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Writing an Access Essay to your Individual Christian University

Writing an Access Essay to your Individual Christian University

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p>Writing of academic documents necessitates a great deal of things that must be taken under consideration. Therefore, here we are going to be discussing only how to compose I-Search article for English course therefore you get a rough idea on the easiest way to handle […]

To Begin a Powerful Essay

To Begin a Powerful Essay

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p>If you would rather make an outstanding application essay founded on the difficulties that you ran into in high school, keep on reading. Students utilize the incorrect faculty tackle labels. They use the on-line application but neglect to request advice from their high school counselor. Students who’d like to […]

Mental Im Sorry Characters

Mental Im Sorry Characters

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p>The coverpage should feature the title of the investigator as well as the essential times about the essay. The types I Have underlined function more dramatically within the essay writing part. School documents aren’t restricted to narratives. Meeting essays help it become possible that you use people as your own […]

To Be A Leader

To Be A Leader

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p>It’s ordinarily educated to pupils within their college days. I am very sure that I bought our background set three decades ago and we’re still utilizing it also within our high school decades Ordinarily, pupils within the higher college Language course know one another, some for a few years. These […]

Are Business Writing Crucial

Are Business Writing Crucial

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p>Your composition must be planned within just how it has a coherent and orderly arrangement. This can make the fundamental bones and outline of your own article. The essay outline can assist you to place your ideas with one another, and possess an obvious notion by what the composition should […]

How to Write an Essay as a Way to Win the Best Purchase

How to Write an Essay as a Way to Win the Best Purchase

Certainly one of the best ways to save a great deal of dollars and make some free money is always by submit an essay to the Top Buy . The article will be accompanied by one essay submitted by the student in […]

Best Essay Writing Tips

Best Essay Writing Tips

The best essays are those which go beyond just the reading of text. What can make your documents more impactful is how that you put them together. You have to have a proper strategy that will allow you to write better and also be able to get maximum attention from a […]

How Can You Write My Essay Canada?

Do you want to create my essay Canada? Have you been given the chance to study in Canada? You could be in the road to being a citizen of Canada. The U.S. is providing international studies opportunities for international students.

How do you find out whether you are eligible with this chance? The U.S. State […]

NCBI Taxonomy 数据库更新,提供lineage、host信息

我们分析metagenome数据离不开使用NCBI的Taxonomy数据,NCBI Taxonomy 提供了一棵物种树,其实每个节点(Node)都分配了一个数字标识符,可以唯一描述一个系统分类信息。

NCBI Taxonomy 数据库提供了一个 taxdump.tar.gz, 并记录了节点的描述信息(names.dmp)以及树的上下游信息(nodes.dmp), 刚刚发布的更新版本提供了额外的lineage信息(rankedlineage.dmp) 以及 host 信息。

另外NCBI已经不再给Strain水平分配这种数字标识符,所以NCBI Taxonomy 提供了 typematerial.dmp 文件用于关联种和菌株(strain)的映射关系。

利用新的数据库我们可以很容易对一些短序列分类器进行注释, 常用的操作如下:

1、 格式化数据库,一般可以使用 tsv-utils

cut -f1,5 fullnamelineage.dmp | sed ‘s/ $//’ >fullnamelineage.db cut -f1,5 taxidlineage.dmp | sed ‘s/ $//’ >taxidlineage.db cut -f1,3 host.dmp >host.db

2、 典型使用场景

下面以Kraken为例子,介绍如何格式化为有效信息, kraken的结果:

C E00552:27:HJ2JYALXX:4:1101:5233:1801 435590 203 816:40 435590:21 A:31 435590:13 0:53 […]

taxon-utils之NCBI Taxonomy 标识符lineage注释: taxon-translation

一、引言:

本文介绍一个小工具,taxon-translation, 使用场景:

需要将NCBI Taxonomy数据库的数字标识符转换成整个Lineage信息。

taxon-utils 仓库地址: https://github.com/jameslz/taxon-utils

二:应用 2.1 数据库格式化 taxon-db

taxon-db程序将NCBI的Taxonomy数据库的 node.dmp 和 name.dmp 合并成一个文件。

执行方法:

taxon-db nodes.dmp names.dmp >ncbi.map gzip ncbi.map

ncbi.map 也可以从 taxon-utils 仓库下载, ncbi.map.gz(版本为2017-09-15)链接。

2.1 数据库格式化 taxon-translate

taxon-translate 命令行接口比较简单:

$ taxon-translate Usage: taxon-translate [options] <ncbi-map> <tab> Options: -c INT target col for taxon translate, default: 1 -v print version number […]