Notably, a single pipeline using BWA-MEM and GATK-HaplotypeCaller performed comparable to the pipeline ensembles for 'callable' regions (~97%) of the human reference genome. While a single pipeline is capable of analyzing common variants in most genomic regions, our findings demonstrated the ...
PacBio whole genome sequencing analysis solutions allow you to generate gold-standard reference genomes through de novo assembly, phase haplotypes and call all structural variant types.
Whole exome sequencing variant analysis pipeline used to analyze the data published in the following manuscript- Gogate A, Kaur K, Goodspeed K, Evans P, Morris MA, Chahrour MH. The genetic landscape of autism spectrum disorder in an ancestrally diverse cohort. npj Genomic Medicine (2024) (Acc...
J. et al. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infect. Dis. 18, 608 (2018). CAS PubMed PubMed Central Google Scholar Kohl, T. A. et al. MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis...
Exome sequencing is a targeted sequencing approach that is restricted to the protein-coding regions of genomes. The exome is estimated to encompass approximately 1% of the genome, yet contains approximately 85% of disease-causing mutations [1]. For genetic re...
Usually, the algorithms of MuTect, VarScan and Genome Analysis Toolkit are applied to identify the variants. However, one of these algorithms alone results in incomplete genomic information. To address this issue, the present study developed a systematic pipeline for analyzing the whole exome ...
Sequencing and bioinformatics analysis pipeline of CNV-seq and WES combined analysis to detect alteration related to congenital structural anomalies. QC quality control; WES whole-exome sequencing; CNV copy number variation; XHMM eXome Hidden Markov model. Additional file 2: Figure S2. Distribution of...
Whole Genome Sequencing (WGS)refers to the high-throughput sequencing of the entire genome, allowing for the analysis of variations between different individuals, as well as the annotation of single nucleotide polymorphisms (SNPs) and genomic structural features. WGS, owing to its comprehensive nature...
The final assembly generated a circular genome sequence without gaps. 2.2. Genome prediction and annotation Protein coding sequences were predicted using the automated pipeline MAKER2 (v2.31.9) [16]. We ran the first iteration of MAKER2, combining data for known mRNAs and proteins and the ab ...
Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling. qualityvariantswhole-exome-sequencingngs-pipelinefastqctrimmomaticquality-scorestile-quality ...