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assay-validation

bk_dvgs

These are the codes we used to generate figures and tables for the BK DVGs paper.

cfdna_hunter

cfdna_pipeline

clomp

:horse: CLinically Okay Metagenomic Pipeline :horse:

cmv-nipt

Reproducible code for the publication "High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights is exceptionally fragmented nature"

covid19-rnaseq

Code used to generate figures for Lieberman et al. 2020

covid_swift_pipeline

demux

Short pipeline for demuxing PacBio files

green_monkey_grna_search

Human gRNA libraries are available through GeCKO but none (that are affordable) exist for the Green Monkey. Biologically, we're close enough to the green monkey that there should be adequate sequence homology in at least some of these targets. Here, I search for human gRNAs that can be found in the Green Monkey genome.

greninger-lab.github.io

hadv_phf_typing_db

Human adenovirus typing database

hpiv3-hn-secondary-structure

Characterizing the HPIV 3 HN gene RNA secondary structure

hpiv3-iterative

hrv_epidemiology

hrv_longitudinal

Files and pipelines used to generate figures

hrv_pipeline

HRV (human respiratory virus) Pipeline is a bioinformatic pipeline for the analysis of Illumina Next-Generation-Sequencing (NGS) for the discovery and GenBank submission of Human Respiratory Virus Genomes.

impaired-tprk-antigenic-variation

Impaired TprK Antigenic Variation Supplementary FIles

lava

LAVA: Longitudinal Analysis of Viral Alleles

lieber_iav_4fiu_supplemental_data_1-4

Supplemental Data 1-4 for: Influenza A virus resistance to 4’-fluorouridine coincides with viral attenuation in vitro and in vivo

longitudinal_sarscov2

longitudinal_tprk

mev-brain-organoids

Measles virus fusion glycoprotein regulates infection and spread in the central nervous system in the presence or absence of innate immunity

mpxv_wgs

A nextflow pipeline for monkeypox virus consensus genome assembly and variants calling

nf_mpxv_f13l

A nextflow pipeline for MPXV consensus genome assembly and F13L variants calling

phipseq

rad_assembler

Nextflow pipeline for Reference Assisted De novo assembling whole genome shotgun sequenced viruses.

rava_pipeline

revica

A reference-based viral consensus genome assembly pipeline

rsv-wa-2022