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Showing 20 open source projects for "process"
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually. -
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MaxBin
An automatic tool for binning metagenomics sequences
...For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
...Currently CSBB provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience. -
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BioC
We describe a simple XML format to share text documents and annotation
... - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining. -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
...However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. Contigs are generated using different assembly algorithms and then merged together to achieve longer continuity. Re-aligning all the reads back to the draft contigs and recalibrating each sequence base achieves a final consensus. Using finished clones for QC, the pipeline is able to obtain assemblies with clone coverage of 99.7% and consensus base quality of Q39. ... -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication... -
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The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
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FIAP
Fully Integrated Annotation Pipeline
...FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows users to annotate, for example, draft genome contigs or different genomes concatenated in multi-fasta file in a single step. FIAP works on all UNIX-like operating systems (tested on Ubuntu 14.04 LTS and Mac OS 10.9.4). -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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basecv
BCV is DNA base caller with vocabulary
The Base Calling with Vocabulary (BCV) software package is intended for analysis of direct (population) sequencing chromatograms using known vocabulary sequences similar to the target DNA. The current version of BCV can only process chromatogram files obtained on Applied Biosystems capillary sequencing machines (ABIF file format). -
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
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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.
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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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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates.
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DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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A set of tools to process and analyze Fasta files. This project is inscribed in the field of Proteomics.
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