Search Results for "assembly source code" - Page 6
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Showing 246 open source projects for "assembly source code"
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IQuant
A pipeline for quantitative proteomics based upon isobaric tags
...This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/". -
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A Scalable Multicore Code for RNA Secondary Structure Prediction
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EducationalLCS
eLCS - Educational Learning Classifier System
Educational Learning Classifier System (eLCS) is a set of learning classifier system (LCS) educational demos designed to introduce students or researchers to the basics of a modern Michigan-style LCS algorithm. This eLCS package includes 5 different implementations of a basic LCS algorithm, as part of a 6 stage set of demos that will be paired with the first introductory LCS textbook. Each eLCS implementations (from demo 2 up to demo 6) progressively add major components of the entire... -
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Percolator, binary downloads
Binary download site for percolator the proteomics post processor
Binary download site for the proteomics data post processor percolator. The source code is hosted on git hub, https://github.com/percolator/percolator -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
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CSEA
Correcting Structural Errors After Genome Assembly
CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com -
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mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more
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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.
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bioluminescence
A java library for polymorphic genome assembly.
Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial... -
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FluxModules
Module Computation for Metabolic Networks
Genome Scale Metabolic Networks are complex systems, Modules help to break them down and hence ease understanding and algorithmic complexity. FluxModules is a toolbox with code for module detection and module visualization. -
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs... -
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PASHA: Parallelized Short Read Assembly
One of the fastest parallel short read assemblers for large genomes.
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates... -
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Framework for individual and population genome assembly and discovery of genetic variants from sequence reads.
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A pipeline to revise a genome sequence of a prokaryotic sample via an iterative backbone remapping and local assembly method.
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Musket - short read error corrector
a parallel short-read error corrector for Illumina sequencing
Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates... -
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primeScaff is intended to automate the sometimes tedious process of manually designing specific primer pairs around gaps of genomic scaffolds and speedup the genome finishing stage of a genome sequencing project. It incorporates de-novo repeat finding using RECON to avoid as much as possible designing primers in repetitive regions and offers the possibility to easily fine-tune the primer design options using primer3. It outputs the repeat, gap and primer annotations in gff2 and gff3 to...
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trimMate is a tool to remove junction adapters as well as sequencing adapters from mate pair libraries and trim the sequences accordingly. It works on fastq files generated by next generation sequencing (NGS) machines. The release is source code only, please download from version control.
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CDSbank
multi-sequence extraction, filtering & formatting
CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical... -
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SpeedyQuant
Quantifies DNA, RNA or protein bands in agarose or acrylamid gels.
...When calculating the relative strength of each band (% of most prominent band) it takes the background noise into account. This leads to accurate and comparable results. Several options can be used to tune the detection process. Here we provide the source code of the program (Perl script) that can be run on any OS with Perl installed (e.g. the freely available Strawberry Perl). A Win-64bit executable is available at: www.foreach-bioinformatics.de -
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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
...You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window. -
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Mix
Mix is a tool to combine multiple assemblies from NGS data.
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the... -
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ClearCanvas
Open source DICOM and RIS/PACS informatics platform
Open source code base for enabling software innovation in imaging. The extensible and robust platform includes viewing, archiving, management, workflow and distribution of images as well as an open architecture for core competency tool development.
