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