Projects

samtools

SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide efficient utilities on manipulating alignments in the SAM format.

bio-bwa

Exome Variant Analysis

Exome Variant Analysis Pipeline (NGS Data). Developed in R language, calling external programs for specific tasks. It can be run in parallel using many processors from the same machine, and can be easily extended to run in computer clusters (HPC). Still in its early stages, it's a work in ... [More] progress that is being used already for production in some research centers. Features: * Quality Control * Mapping in a reference genome * Tasks related to variants: ** Calling ** Filtering ** Annotating ** Reporting effects and basic statistics * Sending an email once the run is finished. More information: ueb(a)vhir.org [Less]

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

Blat-like Fast Accurate Search Tool

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

extellect-utils

A free library of helpful classes that (at the time of writing) I feel are missing from the major libraries such as Microsoft's .NET Framework, Spring.NET and log4net. These types are intended to increase your productivity by letting you reuse something that somebody else has already written ... [More] and unit tested. Please give me any feedback you might have; negative is welcomed as much as positive at this stage! Jono [Less]

microbial-phenotype-database

The Microbial Phenotype Ontology and Database is an effort to bring a well-defined controlled vocabulary to the assignment of properties to various microbes (predominantly Bacteria & Archaea). Aside from a formal ontology of terms, software and human curation of term-specie associations are being developed.

sequencing

This project sequences a give set of DNA sequences against Arabidopsis CDS file in TAIR database. It is useful if you want to know how good is your PCR results. The inputs are

MicroRNA Discovery By Deep Sequencing

MIREAP is a tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

Vancouver Short Read Analysis Package

This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.