Sequencing

SeqGenome Browser, a mini cross-platform local genome browser, was designed for visualizing next-generation sequencing data. It is light, fast and easy to use. Platforms: Windows, Mac, Linux

Timina is a Java web-based application for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences. Platforms: Mac, BSD, Linux

The Unix::ConfigFile module provides a base class from which the other Unix::*File modules are derived. It provides some basic facilities like file opening, locking, and closing. You do not need to use this module directly unless you are developing a derived module for an unsupported... Platforms: *nix

MIDesigner (MID Intelligent Designer) is a utility to design multiplex identifier (MID) primers for use in sequencing projects. Thus, it is similar in intent to Barcrawl. Platforms: Windows, Mac, Linux

WRITESCF writes SCF formatted files.SCF format files are used to store data from DNA sequencing instruments. This version of WRITESCF only adds the raw traces to the SCF files, it does not write the bases or scores. Platforms: Matlab

ScNet is a useful .Net component developed to enable you to build applications for job scheduling. This component has been tested in various development tools (including but not limited to Visual Studio 2005 and Visual Studio 2008). This component ensures a fast and easy way to build and... Platforms: Windows

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project. Platforms: Windows, Mac, Linux

It will help program tweening effects, animations, and transitions.It is comprised of 4 key classes: GTween (tweening engine), GTweenTimeline (time control features), GTweenFilters (useful in tweening filters) and GTweeny (light version of GTween).Here are some key features of "GTween":dlTE... Platforms: Flash

cutadapt is used to remove adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs. News March 16, 2011: cutadapt v0.9.3 has been... Platforms: *nix

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the... Platforms: Mac

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies... Platforms: *nix

Cirklz is a probabilistic step-sequencer for Native Instruments Reaktor 5. It has a simple interface, that produces complex loops that never repeat. Use it to control other softsynths, hardware synths, fx and drum machines. Features # 4 track sequencer # MIDI Out # Probability sequencing # Easy... Platforms: Mac

dnaLIMS is a state-of-the art web based laboratory information management system used to track and manage core facility workflow in high throughput environments. Its database and process flow can be customized to your core facility requirements. dnaLIMS process flow is used to capture DNA... Platforms: Mac

CB-Commander is a plugin based tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface. Platforms: *nix

LividSampler offers you a minimum of controls and options, in order to help you have as much fun as possible. The standalone version can be used as a simple application, and may be preferred for setting up file assgnments and presets, as it adds drag-drop capability for sound files. Either drag... Platforms: Mac

Genomecomb is a package for the analysis of complete genome data. It can be used to compare, annotate and especially filter the results of complete genome sequencing. Platforms: *nix

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based... Platforms: Mac

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'. Features . Alternative expression analysis . WTSS/RNA-Seq library quality assessment . Gene expression analysis . Novel transcript discovery . Visualization of... Platforms: *nix

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies This tool aims to identifying structural variations with both clustering and... Platforms: *nix

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, this code base was released as open source in 2006 by Celera. Platforms: *nix