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Data formats, Data management, Sequence data processing 13amp A virtual FUSE filesystem for on-the-fly CRAM-to-BAM conversion. Annotation AceDB Acedb is a database system developed specifically for handling genome and bioinformatic data, it includes many powerful tools for the ... Analysis ADaM ADaM (Adaptive Daisy Model): an R package for discriminating between core fitness and context-specific fitness genes in large-scale gene essentiality ... Analysis Ag1000g The Anopheles Gambiae 1000 Genome project is a global collaboration using whole genome deep sequencing to provide a high-resolution view ... Analysis Alfresco FRont-End for Sequence COmparison - The aim is to develop a new visualisation tool that allows effective comparative genome sequence analysis. Analysis Alien_Hunter Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable ... Analysis AMELIA - Allele Matching Empirical Locus-specific Integrated Association AMELIA is a program that employs allele matching to analyse the effects of rare variants within a specific locus. Analysis Ariba A software application that identifies anitbiotic resistance genes by running local assemblies. Analysis ARIEL accumulation of rare variants integrated and extended locus-specific test Database software ARNIE - AVEXIS Receptor Network with Integrated Expression ARNIE is an online database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with ... Annotation Artemis Genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the ... Annotation, Visualisation Artemis Comparison Tool (ACT) ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. Analysis AutoCSA AutoCSA is a mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. Analysis, Data formats, Sequence data processing bam2cram-check This is a tools for comparing a BAM file to a CRAM file, after converting from one format to the ... Annotation, Visualisation BamView An interactive Java application for visualising read-alignment data stored in BAM files. Tool BASiCz - Blood Atlas of Single Cells in zebrafish BASiCz - Blood Atlas of Single Cells in zebrafish Data management baton Client programs and API for use with iRODS (Integrated Rule-Oriented Data System). Analysis, Laboratory management BD Influx index data exporter BD Sortware for the Influx stores all the index data inside the .fcs file, however the common analysis tools (FlowJo, ... Laboratory management BD Influx index file counter When requested by management for statistics on index sorting by our customers we wrote this script. It will trawl though ... Analysis, Laboratory management BD Influx sort layout template program This python script applies predefined sort templates to the BD Influx workspace. It can also take designs from Excel and ... Laboratory management BD Influx workspace renamer BD Sortware for the Influx names all its files with non-descriptive names. When backing up and cleaning our PC we ... Analysis Bio-Tradis A set of tools to analyse the output from TraDIS analyses. Analysis, Sequence data processing Biobambam Tools for early stage NGS alignment file processing including fast sorting and duplicate marking. Analysis BioView BioView was born out of the Standalone AutoCSA mutation detection project. Analysis BLAST The Sanger Insitute makes available to researchers a number of blast indicies. Most of these are for microbrial pathogens but ... Analysis BOAT BOAT (Bayesian Overlap Analysis Tool) identifies variants that are associated with two traits and tests for enrichment (i.e. whether ... Data formats CAF Common assembly format (CAF). Analysis Cancer Genome Browser A fully-featured genome browser for cancer genetics Analysis CAROL A combined functional annotation score of non-synonymous coding variants Analysis CCRaVAT & QuTie CCRaVAT (Case-Control Rare Variant Analysis Tool) & QuTie (Quantitative Trait) Analysis, Visualisation Cell Model Passports Database A Hub for Preclinical Cancer Models - Annotation, Genomics & Functional Datasets Analysis, Visualisation cell2location Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model) Pipeline management, Sequence data processing, Visualisation Chromoview Chromoview is a tool for viewing clone tiling paths on chromosomes. It includes data on genomes maintained by the Genome Reference ... Analysis Circlator A software toolkit to circularize genome assemblies. Analysis, Sequence data processing, Statistical and population genetics cloneHD High-definition reconstruction of clonal composition Analysis CnD cnD is a program to detect copy number variants from short read sequence data. Analysis COMET COMET (Corrected Overlap and Marginal Enrichment Test) is a computationally efficient method for identifying SNP features (e.g. functional annotation) ... Clone requests Conditional Knockout Plasmids Data management, Development, Pipeline management, Sequence data processing Cookie Monster Cookie Monster is a tool for triaging the huge amounts of sequencing (and related) data by its metadata, from various ... Database software COSMIC COSMIC, the "Catalogue Of Somatic Mutations In Cancer" is an expert-curated database encompassing the wide variety of somatic mutation mechanisms causing ... Database software, Visualisation COSMIC-3D COSMIC-3D provides interactive 3D visualisations of more than 8,000 human proteins displaying cancer mutations. Analysis, Statistical and population genetics, Visualisation COVID-19 Genomic Surveillance This website shows how SARS-CoV-2 lineages have changed in frequency over time across England. Laboratory management, Pipeline management COVID-19 Genomics UK (COG-UK) Protocols The Institute is contributing a range of protocols on all aspects of large-scale, nation-wide virus sample and metadata collection, preparation, sequencing, ... Data formats CRAM CRAM is a more highly compressed alternative to the BAM and SAM DNA sequence alignment file formats. Analysis CRAWL2 A data mining tool for the purpose of querying a sequence and annotation data source, Java based. Analysis CRISPR GUARD Finder CRISPR GUARD is a method for reducing off-target editing by Cas9 and base editors. Clone requests CRISPR-Cas9 Resources CRISPR-Cas9 Resources. A clone request should be submitted using the electronic form using the link below; this will automatically generate ... Analysis, Visualisation CRISPRcleanR An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting Analysis Cross_genome Cross_genome is a package to build up genome assembly scaffolds using cross-species synteny. Data formats, Data management, Sequence data processing Crumble Crumble - Lossy compression of DNA sequence quality values Data formats DAS Distributed annotation service Database software DBCon DbCon provides a simple interface to DBCP, offers distributed pooling configuration and provides a clean layer of separation between Java ... Database software DECIPHER - Mapping the Clinical Genome DECIPHER is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER ... Analysis DecoyPYrat DecoyPYrat - Fast Hybrid Decoy Sequence Database Creation for Proteomic Mass Spectromtery Analyses Analysis Dindel: Accurate indel calls from short-read data Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It is ... Analysis Discrete Distributional Differential Expression (D3E) D3E is a method for identifying differentially expressed genes from single-cell RNA-seq experiments. D3E compares the full distribution between two ... Annotation DNAPlotter An interactive Java application for generating circular and linear representations of genomes. Analysis, Data management, Sequence data processing, Statistical and population genetics dNdScv dNdScv tool uses dN/dS methods to quantify selection in cancer and somatic evolution Development, Systems administration docker-proxify docker-proxify creates a container environment in which outbound connections are transparently proxied through a proxy server. Analysis Doublescan Doublescan is a program for comparative ab initio prediction of protein coding genes in mouse and human DNA. Analysis EMu EMu is software for inferring the mutational signatures present in a number of cancer mutation sets. Database software Ensembl Genome Browser The Ensembl project creates evidence-based annotation of genome sequences and integrates these data with other biological information. All of Ensembl' ... Analysis, Database software, Statistical and population genetics, Visualisation Epicollect5 Mobile and Web application for free and easy data collection Analysis Eponine Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent ... Clone requests ES Cell Lines Resources available Analysis, Sequence data processing, Visualisation Evoker a graphical tool for visualising genotype intensity data in order to assess genotype calls as part of quality control procedures ... Analysis, Gene finding, Ontology Exomiser The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a ... Analysis FastBAPS A fast solution to cluster genetic sequences Analysis, Laboratory management Flow Cytometry Tools To help with the operation of the flow cytometry facility we have written a range of Python scripts to automate ... Analysis, Sequence data processing, Visualisation Gap5 Gap5 is a DNA sequence assembly visualiser and editing tool. Gene finding GAZE GAZE is a tool for the integration of gene prediction signal and content sensor information into complete gene structures. Analysis GDSC: Genomics of Drug Sensitivity in Cancer The GDSC database facilitates the identification of molecular features of cancers that predict response to anti-cancer drugs. Database software GENCODE The aim of GENCODE is to annotate all evidence-based gene features in the human and mouse genomes at high accuracy. ... Database software GeneDB A genome database containing the latest sequence data and annotation/curation for organisms sequenced by the Pathogen group. Analysis GeneSpy Simple and fast gene-protein visualisation and editing. Analysis Genevar (GENe Expression VARiation) Genevar is a platform of database and web services designed for data integration, analysis and visualization of SNP-gene associations in ... Analysis, Database software gEVAL - Genome Evaluation Browser Genome Assembly Evaluation Browser Annotation gff3toembl This software converts GFF3 files from the annotation tool Prokka into a format that is suitable for submission to EMBL. Analysis GLIDERS Genome-wide LInkage DisEquilibrium Repository and Search Engine Analysis GRAFT GRAFT (Genomic Rearrangement Assembly For Tumours) is an algorithm designed to time rearrangements. Analysis Gubbins Genealogies Unbiased By recomBinations In Nucleotide Sequences Analysis Gubbins Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) can be used to identify recombination. Annotation GWAVA Genome Wide Annotation of VAriants - a functional annotation tool for non-coding sequence variation Analysis, Sequence data processing, Statistical and population genetics Hail analysis pipelines Hail based analysis pipelines for HG projects: pipelines for QC of genome - sequenced cohorts, and GWAS after QC. Designed to ... Analysis Hexamer Scans for likely coding regions using 6-mers but without deriving information from base composition. Development, Systems administration Hgi Cloud Terraform and ansible codebase to provision clusters (e.g. hail/spark) at Sanger. The framework can be used to provision ... Data formats, Database software, Development, Ontology hypr hypr - Research and development of hypermedia information systems. Analysis Illuminus The genotype calling algorithm Analysis Image Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments. Visualisation Immune Interaction An interactive atlas of immune cell receptor interactions in the human body Tool io_trace Io_trace system call traces a process and reports the amount of I/O performed to each file, socket or file ... Clone requests IPB A clone request should be submitted using the electronic form using the link below; this will automatically generate an email ... Analysis IVA A de novo assembler designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. Analysis KATE A program that analyses the effects of low frequency and rare variants on quantitative traits within a chromosomal region Analysis Krocus Krocus is a software application that can predict MLST directly from uncorrected long reads. Analysis largeQvalue A program for calculating FDR estimates with large datasets. Pipeline management Limber A flexible front end to plate based pipelines in DNA Pipelines Analysis LogoMat-M Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Analysis Logomat-P This is a result of the growing number of well characterised protein families in databases such as Pfam. By adding additional ... Analysis, Visualisation LookSeq LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. Analysis, Visualisation Malaria Cell Atlas The Malaria Cell Atlas is an active project led by the Lawniczak lab to provide an interactive data resource of single ... Analysis Margarita Margarita infers genealogies from population genotype data and uses these to map disease loci. Analysis MascotPercolator MascotPercolator is a software package that interfaces the proteomics spectral identification algorithm Mascot (Matrix Science) with Percolator , a well performing ... Database software, Laboratory management MCMS - Mouse Colony Management System MCMS is a fully-hosted and supported web delivered database (LIMS) for tracking mouse colonies and experimental data. It is currently in ... Database software MEROPS The MEROPS database of proteolytic enzymes, their substrates and inhibitors provides a "one-stop shop" for researchers with an interest in ... Analysis, Sequence data processing, Statistical and population genetics METACARPA METACARPA performs scalable meta-analysis between genetic association studies, both effect-size based and p-value based, while correcting for unknown sample overlap. Data management Metadata-check Metadata-check is a tool for verifying that the metadata in a BAM/CRAM file header is consistent with the metadata ... Phylogenetics MicroReact Easily create Interactive web visualisations using Maps, phylogenetic trees and metadata Data management, Laboratory management Mixtio Reagent creation and barcoding service Analysis MLSTcheck A software application for taking MLST databases from multiple locations and consolidating them in one place so that they can ... Data management, Systems administration mpistat mpistat is a tool for efficiently gathering file system statistics from distributed parallel file systems using a large number of ... Analysis MPRA Design Tool This web-based graphical tool allows for rapid generation of .fa files suitable for MPRA experiments. Analysis MPRAnator A tool for the design of high-throughput massively parallel reporter assays (MPRAs) Analysis Multiple Motif Meta Analysis (M3A) The Multiple Motif Meta Analysis (M3A) method can be used to identify enriched and de-enriched DNA motifs from a collection ... Analysis NestedMICA NestedMICA is a method for discovering over-represented short motifs in large sets of strings. Typical applications include finding candidate transcription ... Analysis, Pipeline management Nextflow-RNASeq A bioinformatics analysis pipeline used for RNA sequencing data, written in the new nextflow DSL2 language syntax, leveraging nextflow modules. Analysis NPG NPG in Sequencing Informatics develops, maintains and runs tracking, analysis, qc and archival software to support the Illumina sequencing and ... Analysis, Statistical and population genetics Olorin Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Analysis, Statistical and population genetics optiCall optiCall is a robust genotype-calling algorithm for calling rare, low-frequency and common variants from SNP microarray intensity data. Analysis Optimist Optimist is a simple software package for inferring positive selection from marker dynamics in an asexual population. Annotation Otter Otter is an interactive, graphical, genome annotation tool used by the Havana group to produce high-quality gene models. (Otterlace was renamed ... Analysis, Annotation, Sequence data processing PAGIT Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation. Analysis Pairsnp Obtians pairwise SNP distance matrices from multiple sequence alignments Analysis Panaroo A Bacterial Pangenome Analysis Pipeline Analysis, Database software, Phylogenetics, Statistical and population genetics, Visualisation Pathogenwatch Processing and Visualisation of Microbial Genome Sequences in Phylogenetic and Geographical Contexts Clone requests PcDNA3-Kz-HA A clone request should be submitted using the electronic form using the link below; this will automatically generate an email ... Data management, Systems administration PCP (Parallel Copy) A parallel copy program for Lustre. Analysis PEER PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor ... Analysis Pf3k The Pf3k project is a global collaboration using the latest sequencing technologies to provide a high-resolution view of the natural ... Database software Pfam The open access resource was established at the Wellcome Trust Sanger Institute in 1998. Its vision is to provide a ... Clone requests PFlexible Vector Resources A clone request should be submitted using the electronic form using the link below; this will automatically generate an email ... Database software, Gene finding, Ontology PhenoDigm PhenoDigm is an algorithm to prioritise disease gene candidates based on phenotype information. It incorporates the OWLSim mechanism to align ... Analysis Phusion Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads. Analysis Phusion2 Phusion2 is a pipeline for de novo genome assembly using NGS data. It is based upon a strategy called read ... Phylogenetics PhyloCanvas PhyloCanvas is a HTML5 phylogeneric tree viewer written entirely in browser-native JavaScript, using no external libraries, and uses the Canvas ... Analysis PICNIC PICNIC (Predicting Integral Copy Numbers In Cancer) is an algorithm designed to identify copy number segments and genotypes in cancer ... Clone requests PiggyBac Transposase Resources PiggyBac Transposase Resources Analysis Pindel Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution ... Analysis PlasmidTron A kmer based approach for identifying plasmids. Analysis, Annotation, Gene finding, Vector Resources PlasmoGEM - TOOLS Plasmo GEM is a non-profit, open-access malaria research resource, providing tools for the manipulation of Plasmodium genomes, and using them ... Annotation, Data formats, Visualisation PoGo PoGo – Fast Mapping of Peptides to Genomic Coordinates for Proteogenomic Analyses Analysis PopPUNK A tool for clustering genomes Laboratory management PPMS auto email script A Python script to email the last user of the day when they are operating outside office hours using data ... Laboratory management PPMS Batch Booking This is a very simple script takes the bookings or cancellations as inputted into a csv file and books them ... Laboratory management PPMS to HTML A script that queries the PPMS calendar system to produce a sorted HTML file of the day’s schedule. Annotation Production and Curation of Parasite Reference Genomes The Parasite Genomics Group is working on the assembly, annotation and manual curation of several different reference genomes. Analysis, Database software, Visualisation Project Score database Genetic screens to identify cancer dependencies and drug targets Analysis Projector Projector is a program for the comparative, homology based prediction of protein coding genes in mouse and human DNA. Database software ProServer ProServer is a very lightweight DAS server written in Perl. Gene finding PSILC Pseudogene inference from Loss of Constraint. Clone requests PUTK Plasmid Clone requests. Analysis QUASR QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent ... Analysis Quicktree QuickTree allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods. Analysis REAPR A tool that evaluates the accuracy of a genome assembly using mapped paired end reads. Analysis RetroSeq RetroSeq is for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. Database software Rfam - Archive Page The Rfam database is a collection of RNA families. Analysis Roary A software application for rapidly constructing pan genomes from large numbers of prokaryote samples. Clone requests Roland Rad Clone requests Analysis SaffronTree A software application for fast, reference-free pseudo-phylogenomic trees from reads or contigs. Analysis, Annotation, Data formats, Sequence data processing SAMtools / BCFtools / HTSlib SAMtools, BCFtools. and HTSlib are tools for manipulating sequence alignment (SAM, BAM, CRAM) and variant call (VCF and BCF) files. Analysis, Statistical and population genetics Sanger Imputation Service A free genotype imputation and phasing service provided by the Wellcome Sanger Institute. Tool scmap A tool for unsupervised projection of single cell RNA-seq data. Analysis SCOOP Simple Comparison of Outputs Program Data formats, Sequence data processing Scramble Scramble is a DNA sequencing file format conversion tool included as part of the Staden io_lib package. Analysis scRNA-seq analysis course Teaching material the Hemberg group's course on computational analysis of single-cell RNA-seq data Analysis SEER and PYSEER Seuqence enrichment analyis used in Genome Wide Association studies (GWAS) Annotation SeqTools A suite of tools for visualising sequence alignments Tool Sequencescape Web based LIMS written in Ruby on Rails. Data management, Sequence data processing Serapis Archival Management System Serapis manages the ingestion of data into the iRODS-based human genetics data archive at Sanger. Analysis SeroBA A k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references. Tool Shepherd This code performs targeted archiving of the files arising from the analysis of Sanger sequencing projects. Analysis Single-cell Consensus Clustering (SC3) SC3 is a method for unsupervised clustering of single-cell RNA-seq data. In addition to a graphical user-interface, SC3 provides additional ... Analysis SMALT SMALT aligns DNA sequencing reads with a reference genome. Analysis SMIS SMIS ( Single Molecular Integrative Scaffolding ): an assembly pipeline to improve scaffolds using Oxford Nanopore or PacBio long reads. Sequence data processing, Visualisation Snoopy Browser based quality control tool to expedite reviewing predicted variants in next generation sequencing files. Analysis, Sequence data processing SNP-o-matic SNP-o-matic is a fast, stringent short-read mapping software. Analysis SNP-sites Finds SNP sites from a multi-FASTA alignment file. Laboratory management SPrint A printing service for barcoded labels with a WYSIWIG interface Analysis SSAHA Short description of the Software or database that will appear on every page that links to this page. Analysis SSAHA2 SSAHA2: Sequence Search and Alignment by Hashing Algorithm. Analysis SSAHAest ssahaEST: Sequence Search and Alignment by Hashing Algorithm ssahaEST is a software tool for very fast matching and alignment of ... Analysis ssahaSNP ssahaSNP is a tool for the detection of SNPs and short indels using the first generation capillary sequencing reads. Analysis ssahaSNP ssahaSNP: Sequence Search and Alignment by Hashing Algorithm ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels ... Laboratory management STAN - Spatial Transcriptomics Analysis A LIMS system to support and guide users in the lab providing the Spatial Genomics services. Data management, Pipeline management Tabula Tabula is a tool for recording and analysing command line sessions. Data formats, Development, Systems administration tarbomb Disposal Extract a tar archive, defusing any tarbombs. Data management, Systems administration Tarchecksum Tarchecksum checks that all the files within a tar archive are identical to the files on disk in the directory ... Data management, Pipeline management, Systems administration teepot teepot is a buffered version of the unix tee command. Clone requests The c-Maf WT and c-Maf Mutant Plasmids Clone request submissions. Database software Tiffin Tiffin is a database of predicted regulatory motifs and predicted functional sites ("motif instances") on genome sequences. Annotation, Visualisation TrackHub Generator Generates and updates track hubs for use with the Ensembl Track Hub Registry. Database software TreeFam TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the ... Analysis Turbo SLoMo: high throughput protein modification localisation Turbo SLoMo is a modified version of SLoMo a PTM site localisation tool created at Birmingham University. Database software VEGA Genome Browser VEGA displays all of the manual annotation from the HAVANA team. Data management, Database software Weaver Browser-based Shiny frontend to view internal Lustre volume reports. Analysis WGE - CRISPR design tool WTSI Genome Editing (WGE) is a website and database that provides tools for designing genome editing of human and mouse genomes ... Analysis, Database software, Ontology, Visualisation WormBase and WormBase ParaSite WormBase is the model organism database of C. elegans and other nematodes. The related resource WormBase ParaSite, is a portal ... Data management, Laboratory management XDP sort stats The BD Influx has a very useful feature that automatically saves sort statistics for every run. The XDP does not ... Development xiongxiong Bearer token codec library. Annotation ZMap ZMap is a genome browser written in C++ with the aim of providing fast access to high volume data. Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA. 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