使用其Xpress修剪其区域的qiime2插件

q2-itsxpress的Python项目详细描述


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作者

  • Adam R.Rivers,美国农业部,农业研究处
  • 凯尔·C·韦伯,美国农业部,农业研究处

引文

里弗斯AR、韦伯KC、加德纳TG等。itsXpress:快速修剪的软件 具有标记基因质量分数的内转录间隔序列 分析F1000研究2018,7:1418。doi:10.12688/f1000research.15704.1

简介

内部转录间隔区(its)是小亚单位之间的一个区域。 以及大亚单位rrna基因。是一种常用的系统发育标记 真菌和其他真核生物。its包含5.8s基因和两个变量 长度间隔区域。在扩增子测序研究中,通常的做法是 修剪保守(SSU、5、8S或LSU)区域。Bengtsson Palme等人(2013年) 为此发布了一个软件包ITSx

q2_itsXpress通过在 齐梅2。q2_itsXpress是独立命令的qiime2插件版本 线路实用程序ITSxpressq2_itsXpress旨在支持 精确的序列变体而不是otus。这种新的排序方法 纠错需要每个序列的质量分数数据,所以每个输入 必须修剪序列。它的Xpress通过获取FastQ数据, 取消复制序列,然后使用 嗯搜索。分析结果并返回修剪过的文件。ITS1, 可选择its2或包括5.8srrna基因在内的整个its区。 itsxpress使用itsx的hmm模型,因此结果几乎相同。

需求/依赖关系

Q2_itsxpress安装

  1. 激活Qiime2 conda环境
source activate qiime2-2018.8
  1. 使用BioConda安装q2-itsXpress。请确保在qiime2环境中安装q2-itsxpres。
conda install -c bioconda itsxpress
pip install q2-itsxpress
  1. 在qiime2环境中,刷新插件。
qiime dev refresh-cache
  1. 检查是否安装了itsXpress插件。您应该会看到与下图类似的输出。
qiime itsxpress
../../screenshot.png

用法

在qiime2中,您可以使用以下命令修剪成对或单端读取

qiime itsxpress trim-pair

qiime itsxpress trim-pair-output-unmerged

qiime itsxpress trim-single
  1. qiime itsXpress单装饰
This command takes single-end data and returns trimmed reads. The sequence may have been merged previously or have been generated from a long read technology like PacBio. Merged and long reads trimmed by this function can be used by Deblur but only long reads (not merged reads) trimmed by this function should be passed to Dada2. Its statistical model for estimating error rates was not designed for pre-merged reads.
Command-requirementDescription
–i-per-sample-sequences
  • The artifact that contains the sequence file(s).
  • Either Joined Paired or just a single fastq.
  • One file sequence in the qza data folder.
–p-region
  • The regions ITS2, ITS1, and ALL.
–p-taxa
  • Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P, Q, R, S, T, U, V, ALL.
–p-threads
  • The amount of threads to use.
–o-trimmed
  • The resulting trimmed sequences from ITSxpress in a qza format.
–cluster-id
  • The percent identity for clustering reads, set to 1 for exact dereplication.
  1. qiime itsXpress修剪对
This command takes paired-end data and returns merged, trimmed reads. The merged reads trimmed by this function can be used by Deblur but not Dada2. Its statistical model for estimating error rates was not designed for pre-merged reads, instead use qiime itsxpress trim-pair-output-unmerged.
Command-requirementDescription
–i-per-sample-sequences
  • The artifact that contains the sequence file(s).
  • Either Joined Paired or just a single fastq.
  • One file sequence in the qza data folder.
–p-region
  • The regions ITS2, ITS1, and ALL.
–p-taxa
  • Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P, Q, R, S, T, U, V, ALL.
–p-threads
  • The amount of threads to use.
–o-trimmed
  • The resulting trimmed sequences from ITSxpress in a qza format.
–cluster-id
  • The percent identity for clustering reads, set to 1 for exact dereplication.
  1. qiime itsxpress修剪对输出未合并
This command takes paired-end data and returns unmerged, trimmed reads. The merged reads trimmed by this function can be used by Dada2 but not Deblur. For Deblur use qiime itsxpress trim-pair.
Command-requirementDescription
–i-per-sample-sequences
  • The artifact that contains the sequence file.
  • Only paired will work.
  • Two file sequences in the qza data folder.
–p-region
  • The regions ITS2, ITS1, and ALL.
–p-taxa
  • Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P, Q, R, S, T, U, V, ALL.
–p-threads
  • The amount of threads to use.
–o-trimmed
  • The resulting trimmed sequences from ITSxpress in a qza format.
–cluster-id
  • The percent identity for clustering reads, set to 1 for exact dereplication.

分类键

AAlveolata
BBryophyta
CBacillariophyta
DAmoebozoa
EEuglenozoa
FFungi
GChlorophyta (green algae)
HRhodophyta (red algae)
IPhaeophyceae (brown algae)
LMarchantiophyta (liverworts)
MMetazoa
OOomycota
PHaptophyceae (prymnesiophytes)
QRaphidophyceae
RRhizaria
SSynurophyceae
TTracheophyta (higher plants)
UEustigmatophyceae
ALLAll

示例

用例:从真菌扩增子中修剪ITS2区域 使用两个cpu线程使用PairedSequencesWithQuailty qza对数据集进行排序。 使用的示例文件位于paired.qza下的tests文件夹中。

qiime itsxpress trim-pair --i-per-sample-sequences ~/parired.qza --p-region ITS2 \
--p-taxa F --p-threads 2 --o-trimmed ~/Desktop/out.qza

许可证信息

这个软件是美国农业部的, 农业研究服务,并在创新共享CC0下发布 公共域属性。

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