Paul Gordon's Projects
Conda recipes for the bioconda channel.
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Estimate nucleobase damage from sequencing substitution artifacts
Create cancer bioinformatics reports from metadata and workflow output
Adjust a FastA DNA genome file's ORFs to correct frameshifts by best Diamond match
A scheme for calculating a unique identifier for any human DNA sample with genome/exome data
Supplemental Statistical Tests and Utilities for Kallisto/Sleuth RNASeq Analysis
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Fast signal-level matching for direct RNA nanopore sequencing
Automatically stop a MinION sequencing experiment after a specific amount of data has been collected.
Strip reads from Oxford Nanopore FAST5 files if they meet certain criteria
Nextstrain build for novel coronavirus (nCoV)
A pipeline that can fetch the latest nCoV data from GISAID, transform it, and put it on S3
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Assign SARS-CoV-2 clades in the browser
Targeted subsampling of SARS-CoV-2 genome sequence ensembles used in genomic epidemiology
GPU-accelerated Dynamic Time Warp (DTW) Barycenter Averaging
Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes
Reproduction number Estimation Accounting for Lead time
RNA Sequence Picking After Cutting Enzymatically
Supplemental code for "the architecture of SARS-CoV-2 transcriptome" paper
SquiggleKit: A toolkit for manipulating nanopore signal data
A Jekyll static site generator theme for building lightweight audio tours for exhibitions or museums.
Training models for basecalling Oxford Nanopore reads
Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake
Evaluate mismatch sensitivity of every 3-mer context in a genome to PCR primers