Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. Early detection and in depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Summary: SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. , and a development version isĪvailable from GitHub at: (/DevonDeRaad/SNPfiltR).Īdditionally, thorough documentation for SNPfiltR, including multipleĬomprehensive vignettes, is available at the website: Investigating, visualizing, and filtering SNPs as part of a cohesive andĮasily documentable bioinformatic pipeline. Reduced-representation genomic datasets, SNPfiltR is an ideal choice for These benchmarking results indicate that for most That for moderately sized SNP datasets (up to 50M genotypes withĪssociated quality information), SNPfiltR performs filtering withĬomparable efficiency to current state of the art command-line-based Standard vcf file into an R working environment using the function Which can be easily generated by reading a SNP dataset stored as a All SNPfiltR functions require a vcfR object as input, SNPfiltR extends existing SNP filteringįunctionalities by automating the visualization of key parameters suchĪs depth, quality, and missing data, then allowing users to set filtersīased on optimized thresholds, all within a single, cohesive workingĮnvironment. Here I describe the novel R package SNPfiltR and demonstrate itsįunctionalities as the backbone of a customizable, reproducible SNPįiltering pipeline implemented exclusively via the widely adopted R Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research. The pipeline provides a quick and efficient way to obtain a matrix of read counts that can be used black with tools such as DESeq2 and edgeR for differential expression analysis. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential gene expression analyses. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. This has enabled researchers to answer many biological questions through ``multi-omics'' data analyses. The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon).doi: 10.1093/biomethods/bpaa014 Our peer-reviewed paper is available here: To get information such as Primers, visit their protocol. This protocol is a modified version of Nikki Freed and Olin Silanders protocol. 11 hrs for 12 multiplexed barcoded specimens. Duration of the complete pipeline was approx. We tested the simplified and less time-consuming workflow on confirmed SARS-CoV-2-positive specimens from clinical routine and identified pre-analytical parameters, which may help to decrease the rate of sequencing failures. Subsequently, we applied the Oxford Nanopore Rapid barcoding protocol and the portable MinION Mk1C sequencer in combination with the ARTIC bioinformatics pipeline. We adapted and simplified existing workflows using the ‘midnight’ 1,200 bp amplicon split primer sets for PCR, which produce tiled overlapping amplicons covering almost all of the SARS-CoV-2 genome. The cost per sample accumulates at around 40$, with already isolated RNA. The whole Sequencing can be done in one working day, including the bioinformatic pipeline. We established a protocol for fast, cost efficient Sars-CoV-2 sequencing with little as possible hands-on time (around 3h in total, excluding RNA extraction).
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