viral-genomics
There are 32 repositories under viral-genomics topic.
WrightonLabCSU/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
nf-core/vipr
Assembly and intrahost / low-frequency variant calling for viral samples
hzi-bifo/Quasimodo
QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
jonas-fuchs/virHEAT
Visualize microbial evolution at the SNP level!
agudeloromero/EVEREST
Viral genome assemble and characterisation
gFedonin/VirGenA
A reference guided assembler of highly variable viral genomes
ucsd-ccbb/C-VIEW
This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
broadinstitute/bvas
bvas: bayesian viral allele selection
will-rowe/artic-tools
a set of tools for viral amplicon schemes
quadram-institute-bioscience/uvaia
Reference-based alignment and sequence database search of SARS-CoV-2 genomes.
alfonsomiguelcruz/pgc_btip_topone
TopONE is a project that studies recombination events using topological data analysis. This was made in the PGC-BTIP 2024 internship by Alfonso Miguel Cruz and Claire Angelie Gabisay, and mentored by C.J. Palpal-latoc.
cvisb/cvisb_data
Data portal and API for Center for Viral Systems Biology (CViSB) data
gallardo-seq/MrHAMER
High accuracy single molecule Nanopore reads using the MrHAMER pipeline
khourious/vgapONT
Viral genome assembly pipeline for WGS using ONT
khourious/vigeas
VIral GEnome ASsembly pipelines for WGS
sociovirology/human_influenza_LMGSeq
Linked Multilocus Genotype by Sequencing (LMGSeq) applied to high-throughput quantification of genetic exchange among diverse human Influenza A virus strains
hello-im-aryss/ViralGenomicsApp_Bis15L_R
UC Davis: Data Science for Biologists - R markdown
schultzm/havic
Detect Hepatitis A Virus Infection Clusters
STTLab/HIV-64148
HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.
alepfu/vog-eda
EDA of virus orthologous groups (VOGs) from VOGDB and eggNOG
Alepidoptera7/k-means-to-BLAST-
Uses k-means prediction to ascertain genomic sequences within ambiguously attributed fasta format data. The resulting cluster sequences are used to develop NCBI BLAST requests.
CanCOGeN-V/irida-plugin-viral-amplicon-consensus-variants
Sequence Analysis Pipeline for the IRIDA Platform for Viral Genomes
encacen21/Bioinformatics-Tool-Primer-Design
A bioinformatics tool for designing primers and generating consensus sequences in viral genome analysis. It supports processing multiple aligned genomic sequences, optimizing primers, and visualizing genome annotations.
mkayasth/viralGeneClock--codespaces
Python tool for relative mutation rate of different genes across viral strains.
tomalf2/recombinhunt-cov
RecombinHunt (alias for the software contained in this repository) is a Python library implementing a data-driven novel method for identifying contributing lineages and breakpoints in recombinant viral sequences.
vpeddu/CMV-NIPT
Hunting for CMV and HHV-6 in cfDNA sequence
acharyak184/Kamal-Acharya
Kamal_Acharya
akarazeev/LauzHack19
🇨🇭🦠 Service for pathogens and threats identification in hospital environments - SOPHiA Genetics
biocyberman/viral-ngs
Viral genomics analysis pipelines
caleblareau/hhv6-reactivation
Repository for analyses of HHV-6 reactivation using genomics
giffordlabcvr/NCBI-HCV-GLUE
Extension to HCV-GLUE - contains all published HCV data from NCBI, plus analysis logic for HCV genomes.
Public-Health-Bioinformatics/irida-plugin-micall-lite
Human RNA virus genotyping