⚡ ♒ Rapid prokaryotic genome annotation

✂️ ⚡ Rapid haploid variant calling and core genome alignment

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

Core BioPerl 1.x code

VarDict

scary tools for building CPAN distributions

🌳 Create a tree using Mash distances

💾 📃 "Reads to report" for public health and clinical microbiology

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Phylogenetic and taxonomic analysis for genomes and metagenomes

Core modules used by the GMS

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

The Exome Coverage and Identification Report displays the coverage of every target region in your capture design. It also displays regions below an adjustable coverage threshold.

Detect complex indels from next-generation sequencing reads

Genome assembly/prediction/annotation pipeline for the Linux command line

A Metagenomic Pipieline for Automated Simulations and Analysis of Gene Families (source code)

A collection of Perl scripts to calculate gene-level similarity among annotated genomes as used in Kislyuk et al. BMC Genomics 12: 32 (2011). The scripts can be executed from the command line and t…