VALIDATION_STRINGENCY=LENIENT \ REFERENCE_SEQUENCE=human.fa \ SD=human.fa.dict 4. 去除PCR重复reads —— MarkDuplicates 在NGS测序之前都需要先构建测序文库,通过物理(超声)打断或者化学试剂(酶切)切断原始的DNA序列,然后选择特定长度范围的序列去进行PCR扩增并上机测序。但我们构建测序文库时能用的细胞量并不会...
samtools faidx reference_genome.fa java -jar picard.jar CreateSequenceDictionary REFERENCE=reference_genome.fa OUTPUT=reference_genome.dict 需要注意的是bwa index的默认算法是is,这种建立索引的方式不适合2G以上的基因组,因此这里使用的是另一种算法bwtsw,同时如果是gatk需要注意reference_genome.dict的后缀,没有"...
WGS includes coverage of all coding and non-coding regions, regulatory sequences, and inter- and intra-genic portions of the genome. Then, the sequencing data are aligned to a reference genome for variant analysis, assembled into contigs forde novogenome assemblies, or used for microbial classific...
RNA测序数据分析rna-sequence测序 RNA测序(RNA Sequencing,简称RNA-Seq,也被称为全转录物组鸟枪法测序Whole Transcriptome Shotgun Sequencing,简称WTSS),是基于二代测序技术研究转录组学的方法,可以快速获取给定时刻的一个基因组中RNA的种类和数量。RNA-Seq有助于查看基因的不同转录本、转录后修饰、基因融合、突变/SN...
Estimating telomere length from whole genome sequence data. Nucleic Acids Res. 2014 May;42(9):e75. doi: 10.1093/nar/gku181. Epub 2014 Mar 7. PMID: 24609383; PMCID: PMC4027178.5. Nersisyan L, Arakelyan A. Computel: co...
Nik-Zainal, S., et al., Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature, 2016. 534(7605): p. 47-54.研究人员测了560位乳腺癌患者(556位女性和4位男性)的肿瘤和正常组织的全基因组,共鉴定出93个驱动基因,以及与缺陷DNA修复和BRCA1及BRCA2功能相关的突变标签(...
sequence-search wgs hla hla-database imgt hla-typing Updated May 21, 2019 Java songtaogui / pan-Zea_construct Star 28 Code Issues Pull requests Workflow to construct linear representation of pan genome from deep WGS data and public assemblies wgs pangenome maize Updated Oct 31, 2023 Shel...
Whole genome sequencing (WGS) is a powerful approach that harnesses the advanced NGS technology to sequence an entire genome. It sequences not only all of chromosomal DNA but also DNA contains in the mitochondria. The results contain information of DNA sequence as well as genetic relationships, ...
Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.
1. `gatk CreateSequenceDictionary -R /data/bio-wenzl/hg38_old/hg38.fa -O /data/bio-wenzl/hg38_old/hg38.dict`: - `gatk CreateSequenceDictionary` 是GATK中的一个命令,用于创建一个序列字典文件。 - `-R /data/bio-wenzl/hg38_old/hg38.fa` 指定了参考基因组FASTA文件的路径,这里是hg38版...