Stars
cloc counts blank lines, comment lines, and physical lines of source code in many programming languages.
A utility for downloading TV and radio programmes from BBC iPlayer and BBC Sounds
ggplot2: elegant graphics for data analysis
✂️ ⚡ Rapid haploid variant calling and core genome alignment
🔎 💊 Mass screening of contigs for antimicrobial and virulence genes
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
💾 📃 "Reads to report" for public health and clinical microbiology
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
Practical, reusable scripts for bioinformatics
Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
Filter SAM file for soft and hard clipped alignments
A tutorial for learning de novo assembly
🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
Snakemake pipeline for annotating metagenome-assembled genomes (MAGs) (pronounced mag-pie)
Using Alignment Uncertainty from Many Multiple Sequence Alignments to Create Consensus Trees