Sequencing

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra.

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

OMS is used for sequencing events on a timeline, allowing control of software and hardware for music, video, and demoscene productions. It is fairly similar to trackers, which are music editors, famous for their use in games and demoscene productions.


Platforms: Windows, Mac, Linux

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.PerlPrimer's current features include the following: - Calculation of...


Platforms: *nix, Perl, BSD

Pyrotagger only accepts sequencing reads that have MID sequences (a.k.a barcodes, tags), and all of them must have the same length. When you have no MIDs, or variable-length MIDs, Pyrotagger MID Adjust appends new MIDs or extends existing ones to satisfy Pyrotagger requirements.


Platforms: Windows, Mac, Linux

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

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.


Platforms: Windows, Mac, Linux

SlideViewer is an automatic picture viewer. Just point SlideViewer at directories containing images, and it will sequentially display the images as a slide-show. Convenient controls enable altering the speed, pausing, going-back, as well as sequencing manually.


Platforms: *nix

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

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

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

Welcome to the SRMA home page. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed...


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

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

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

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

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

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