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http://linux1.softberry.com/spldb/SpliceDB.html
Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.
Proper citation: SpliceDB (RRID:SCR_006262) Copy
http://www.sanger.ac.uk/resources/software/peer/
Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.
Proper citation: PEER (RRID:SCR_009326) Copy
https://github.com/sanger-pathogens/Fastaq
Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.
Proper citation: Fastaq (RRID:SCR_016091) Copy
http://www.sanger.ac.uk/science/tools/olorin
An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)
Proper citation: OLORIN (RRID:SCR_002015) Copy
https://www.sanger.ac.uk/science/tools/reapr
Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.
Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy
https://github.com/hemberg-lab/scmap
Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.
Proper citation: Scmap (RRID:SCR_017338) Copy
http://www.sanger.ac.uk/Projects/C_elegans/index.shtml
The Sanger Institute and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis have collaborated to sequence the genomes of both C. elegans and C. briggsae. The completed C. elegans genome sequence is represented by over 3,000 individual clone sequences which can be accessed through this site (or through WormBase). These sequences are submitted to EMBL whenever the sequence or annotation changes (e.g. modification to gene structures) and these submissions are then mirrored to GenBank and DDBJ. These sequences (along with ESTs and proteins) can be searched on our C. elegans BLAST server. WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans. The worm informatics group at the Sanger Institute play a key role in assembling the whole database. They also curate and develop some of the constituent databases that comprise WormBase.
Proper citation: Caenorhabditis Genome Sequencing Projects (RRID:SCR_008155) Copy
http://www.sanger.ac.uk/Projects/Fungi/
Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases.
Proper citation: Fungi Sequencing Projects (RRID:SCR_008524) Copy
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