PathSeq参数基于基因组序列和参考数据库,通过比对和分析DNA或RNA测序数据中的路径信息,来确定样本中存在的微生物种类和数量。它通过检测样本中的路径特征,如代谢途径、细胞结构和功能等,来推断微生物的存在和功能。 PathSeq参数的原理主要包括以下几个步骤: 1. 数据预处理:将原始测序数据进行质量控制、去除低质量序列和...
--microbe-bwa-image pathseq_microbe.fa.img \ #待检测微生物参考基因组的BWA索引镜像 --taxonomy-file microbe.db \ #待检测微生物的分类学文件 --output output.pathseq.bam \ # 包含与微生物参考对齐的所有高质量非宿主读取。 --scores-output output.pathseq.txt # 输入样本的微生物组成表 conda环境下运...
gatk PathSeqPipelineSpark \--input test_sample.bam \ #输入样本的bam--filter-bwa-image hg19mini.fasta.img \ #人类参考基因组的BWA索引镜像--kmer-file hg19mini.hss \ #根据人类参考基因组构建的k-mer库--min-clipped-read-length70\ #设置排除假阳性的阈值,越高则比对到的外源序列越少--microbe-fasta...
gs://gatk-best-practices/pathseq/resources/meats.fa.img gs://gatk-best-practices/pathseq/resources/meats.min2k.db gs://gatk-best-practices/pathseq/resources/pathseq_bundle_readme.txt gs://gatk-best-practices/pathseq/resources/pathseq_host.bfi gs://gatk-best-practices/pathseq/resources/pathseq_h...
PathSeqPipelineSpark老鼠 pathpulse 1 Pathlib介绍 pathlib是跨平台的、面向对象的路径操作模块,可适用于不同的操作系统,其操作对象是各种操作系统中使用的路径(包括绝对路径和相对路径) pathlib有两个主要的类,分别为PurePath和Path。 1.1 PurePath PurePath访问实际文件系统的“纯路径”,只负责对路径字符串执行操作。
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Abstract 949: PathSeq: A comprehensive computational tool for pathogen discovery by deep sequencing of human cancer tissues BACKGROUND: It is thought that pathogens cause a significant fraction of human cancers. However, many of these pathogens are unknown. Our project is based on the premise that...
Hello everyone, When I use the PathSeqPipelineSpark to analyze my datasets, I meet the next issue: ERROR DiskBlockObjectWriter: Uncaught exception while reverting partial writes to file /tmp/blockmgr-a212bfd7-e23c-4634-977e-979a86afe37f/...
This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection. - gatk-workflows/gatk4-pathseq
gatk PathSeqPipelineSpark \--input test_sample.bam \ #输入样本的bam--filter-bwa-image hg19mini.fasta.img \ #人类参考基因组的BWA索引镜像--kmer-file hg19mini.hss \ #根据人类参考基因组构建的k-mer库--min-clipped-read-length70\ #设置排除假阳性的阈值,越高则比对到的外源序列越少--microbe-fasta...