Pinned Repositories
2017-cicese-metagenomics
2020_scWorkshop
Code and data repository for the 2020 physalia course on single cell RNA sequencing.
algo
数据结构和算法必知必会的50个代码实现
bioscript
A repository for some useful bio-scripts.
FMT-donor
This is a script repository for FMT-donor paper.
laca
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
MAC2023
MAC course
microbiome_analysis
Repository for the microbiome analysis
nart
A tool for Nanopore Amplicon Real-Time (NART) analysis.
ONTrapid
ONT assembly pipeline
yanhui09's Repositories
yanhui09/2020_scWorkshop
Code and data repository for the 2020 physalia course on single cell RNA sequencing.
yanhui09/AppStat2020
yanhui09/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
yanhui09/Azimuth
Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency
yanhui09/bbk3_wf
Scripts to run biobakery workflow at KU FOOD
yanhui09/BookChapter-RNA-Seq-Analyses
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
yanhui09/bwt2map
A snakemake workflow to do alignment with bowtie2, and some down-stream analysis
yanhui09/COVIDPBMC
Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection
yanhui09/data-science-learning-resources
A collection of machine learning resources that I've found helpful (I only post what I've read!)
yanhui09/eat_tensorflow2_in_30_days
Tensorflow2.0 🍎🍊 is delicious, just eat it! 😋😋
yanhui09/metagenomics_summer_school
Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in December
yanhui09/yanhui09
My personal repository
yanhui09/sync_utilities
script to sync files between severs
yanhui09/LCPsCluster
The LCPsCluster module for the on-rep-seq
yanhui09/longread_umi
yanhui09/MAGpy
Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
yanhui09/markdownhere4zotero
markdown here zotero 插件
yanhui09/MGV
Supporting code for uncultivated gut virus manuscript
yanhui09/MicrobiomeVis
The repository for microbiome analysis tutorial - MicrobiomeVis
yanhui09/Mosaic
MOSAIC
yanhui09/Nutrition5k
Detailed visual + nutritional data for over 5,000 plates of food.
yanhui09/On-rep-seq
Bulk Typing of Bacterial Species down to Strain Level
yanhui09/open-source-cs-python
Video discussing this curriculum:
yanhui09/parallel-meta
A High Performance Microbiome Analysis Toolkit.
yanhui09/Python-100-Days
Python - 100天从新手到大师
yanhui09/PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
yanhui09/sequitur
Autoencoders for sequence data
yanhui09/shrinksam
C++ program to shrink the SAM file after a read-mapping
yanhui09/viralMetagenomicsPipeline
Pipeline for metagenomic community analysis using DNA isolated from virus-like particles
yanhui09/yanhui09.github.io