Search Results for "assembly source code" - Page 7
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Showing 246 open source projects for "assembly source code"
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Circonspect is a bioinformatic tool to produce contig spectra, useful for the estimating viral diversity in metagenomes. It uses an external assembly program and a bootstrap technique to automate the generation of contig spectra and cross-contig spectra.
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Timina is a Java web-based application for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences.
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parFE is fully-parallel high-performance finite element code targeted to the modeling of trabecular bones in humans. It employs scalable multigrid solvers for efficient solutions on massively parallel computers.
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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denovo_solid_pipeline
Pipeline for small genome assembly using SOLiD sequencing technology
denovo_solid_pipeline (DSP) is a semi automated pipeline for short genome assembly using SOLiD sequencing data. The main features of the pipeline are the optimization of the number of read-correction runs and computational resources via dynamic programming. DSP also has the advantage over the currently available pipeline (denovo2) of generating more contigs suitable for further assembly steps, increasing the chances of detecting sequencing errors and/or polymorphic sites. -
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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DecGPU: CUDA-based Error Correction
The first distributed and parallel short-read error corrector on GPUs
DecGPU (Distributed Error correction on GPUs) is a parallel and distributed error correction algorithm for large-scale short read assembly. It is implemented using CUDA C++ and MPI, running on a GPU cluster. -
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samsn
A tool to handle multi-stage mass spectrometry data
The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn -
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The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.
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MIDA
Mitochondiral Infectious Damage Adaptation (MIDA) model of aging
...Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code. -
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Atlas2Cloud
Atlas2 Genome Analysis Pipeline on Amazon Web Services
This is the backend source code of the Atlas2-Cloud pipeline on Amazon which starts and terminates worker nodes, runs analysis and monitors worker instances. It is PRIMARILY meant to be used through Amazon Web Services (AWS) management console by looking for the public Atlas2-Cloud machine image. Alternatively, the code can also be used for running the pipeline from your computer. -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and... -
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BIGrat
A genome assembly tool for pyrosequencing-based re-sequencing
BIGrat: a genome assembly tool for pyrosequencing-based re-sequencing -
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coords-view
Graphically displays nucmer/mummer mapping results
Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25 -
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...
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A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
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Clinical Evidence Detector
Detector of clinical evidence
This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf -
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RepMiner takes a graph theory approach to the classification and assembly of the repetitive fraction of genomic sequence data. Sequence lengths analyzed by RepMiner can range from full length transposable elements to low coverage sample sequence data.
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports. -
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A phologenetic supertree construction/assembly tool using triplet similarity as the objective function.
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This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.
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Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
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The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
