Tools for Data Analysis

Several tools for data analysis have been developed or are in use by ESGI.

High throughput sequencing analysis tools

The Wellcome Trust Sanger Institute hosts a website to facilitate access to high throughput sequencing analysis tools, acting as an information resource for the project and the wider research community. It contains information about bioinformatics and computational tools available for the analysis of high-throughput genomic data. Please click here to open the link in a new window.

Web-based toolkit designed to process and analyse large-scale small RNA datasets

A web-based toolkit to process and analyze large-scale small RNA datasets has been developed (SeqBuster). Seqbuster is designed to identify and analyze both miRNAs and non-miRNA small RNAs. Seqbuster performs all the steps from adaptor trimming to small RNA annotation of both miRNA and non-miRNA sequences. To access SeqBuster, please click here.

Reliable alignment of bisulphite sequences to a genome sequence: B-SOLANA

B-SOLANA provides a fast and accurate all-in-one approach including alignment and methylation calling of two-base encoding (“colorspace”) bisulfite sequencing data. It performs sequence alignment and methylation calling for two-base encoding (colorspace) bisulfite sequencing. It is based on the established short read aligner Bowtie (Langmead, 2009) and SAMtools, utilities for manipulating alignments (Li, 2009). Please access B-SOLANA here.

pibase tools for validational and comparative analysis of BAM files

pibase validates SNVs by emulating a human user at a viewer: gathering and documenting information, and making a summary decision on the variant genotype and quality. pibase is a command line tool which can be integrated into a pipeline or started interactively from the command line. Please access it here.

Analytical tools for breakpoint characterisation of structural variations

ESGI partner CRG has been working on the development of a tool, PeSVFisher, for the detection of structural breakpoints from whole genome sequencing data. PeSVFisher identifies and provides accurate breakpoints for copy number variants as well as other structural variants like inversions, duplications and translocations. The tool is available here.