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Toolbox for comparative genomics of MAGs

AcinetoScope is an automated, comprehensive bioinformatics pipeline designed specifically for the genomic analysis of Acinetobacter baumannii, a WHO Critical Priority pathogen responsible for devastating hospital-acquired infections. It integrates seven analysis types (MLST, ABRicate, AMRFinder, Kaptive 3, APT, PlasmidFinder, and mutation detection) into a single automated workflow — from FASTA to actionable insights. The pipeline offers both gene-centric and sample-centric reporting, dynamic grouping by typing, and is optimised for HPC, cloud, and container environments.

SMBGC Annotation using Neural Networks Trained on Interpro Signatures

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Utility that performs integrated analyses of 'gene' data (a set of genes or other genomic features) with 'peak' data (a set of regions, for example ChIP peaks) to identify the genes nearest to each peak, and vice versa.

Short Python script (using Biopython library functions) to extract sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given by a column of a tabular file. The output order follows that of the tabular file, and if there are duplicates in the tabular file, there will be duplicates in the output sequence file.