Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

Graph-based mapping of long sequences, noisy or HiFi.

Updated Kraken DB install scripts to cope with new-ish NCBI structure

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

Genome Annotation Without Nightmares

The MG-RAST Backend -- the API server

🐙 A curated database of completed assemblies with taxonomy IDs

Pipeline for analysing intergenic regions in bacteria

A software for the multispecies design of CRISPR/Cas9 libraries

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

Identify phage regions in bacterial genomes for masking purposes

Manipulate FASTA files

A false-positive filter for variants called from massively parallel sequencing

Get microbial sequence data easier and faster

Kraken(2) database based on the GTDB project

🍶 Genome assembly with short sequence reads

Assembly based core genome SNP alignments for bacteria

CRISPR/Cas9 guide RNA Design

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE …

PhylOTU identifies microbial OTUs from metagenomic data

Workflows I find helpful for fungal genome annotation

Fungal Genome Mapping Pipeline

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

Hierarchical Unique Bait Design for simultaneous and specific capture of known and novel targets

GUI for batch primer design with graphical output for PCR and SNP detection

The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format