Stars
BisCEET is a tool to visualize and compare related biosynthetic gene clusters.
BGC-QUAST: quality assessment tool for genome mining software
PanBGC-DB is a comprehensive resource for the exploration of biosynthetic gene cluster (BGC) diversity using a pangenome-inspired framework. It enables users to visualize gene cluster families (GCF…
Long Read-based Microbial genome mining pipeline
A nextflow pipeline for decontamination of short reads, long reads and contigs
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Targeted Detection and Reconstruction of Plasmids
This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.
A new high-resolution long-read metagenome assembler for even noisy reads
Genome-scale protein function classification
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
Follow up to Grace Blackwell's 661k dataset, for 2023
✂️ ⚡ Rapid haploid variant calling and core genome alignment
A tool to circularize genome assemblies
A tool to flip GenBank format DNA records to make sure genes of interest are on the right strand.
Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Predictive Algorithm for Resolving A-domain Specificity
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
BRIG is a cross-platform (Windows/Mac/Linux) application that displays circular comparison images of multiple genomes using BLAST.
BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons 🦠
Predictive Algorithm for Resolving A-domain Specificity by featurising Enzyme and Compound in Tandem
A tool for generating consensus long-read assemblies for bacterial genomes