Bioinformatics Pipelines

COVID-19

A public repository of scientific and media resources of SARS-CoV-2 related COVID-19 maintained by ITER.

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Bioinformatics Pipelines

Under construction. Soon here!

A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing

Alternative Illumina protocol for SARS sequencing (for Ct up to 38)

Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

Broad Institute viral-related pipelines. Several available repositories with scripts and tools for the analysis of viral NGS data

Centre for Genomic Regulation, CRG, public.docs repository, COVID sequences, including fast5 files

Characterization of intra-host SARS-CoV-2 variants improves phylogenomics reconstruction and may reveal functionally convergent mutations

China National Center for Bioinformation (CNCB), 2019 Novel Coronavirus Resource | Genome Variation | Data release statistics

CDC GitHub SARS-CoV-2 Sequencing Resources

CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event

COVID-19 ARTIC v3 Illumina library construction and sequencing protocol

COVID-19 Cell Atlas

Elevated Plasmin(ogen) as a Common Risk Factor for COVID-19 Susceptibility

Emergence of multiple variants of SARS-CoV-2 with signature structural changes

Enrichment workflow for detecting coronavirus using Illumina NGS systems

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?

iVar for for viral amplicon-based sequencing

Katarina Braun GitHub ARS-CoV-2_sequencing repository

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

NCBI GenBank SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences

NCBI GenBank Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome. GenBank: MN908947.3

Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

Quality control of low-frequency variants in SARS-CoV-2 genomes

SARS coronavirus 2 in Viral Zone / Covid-19 genome expression

Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

The global population of SARS-CoV-2 is composed of six major subtypes

Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication