Open Source Unix Shell Bio-Informatics Software
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Unix Shell Bio-Informatics Software
View 59 business solutionsBrowse free open source Unix Shell Bio-Informatics Software and projects below. Use the toggles on the left to filter open source Unix Shell Bio-Informatics Software by OS, license, language, programming language, and project status.
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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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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php -
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Tool for metagenomic viral community profiling
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Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
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Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge
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The WISDOM project is a Grid based production environment used to deploy bio-informatics large scale applications.
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BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
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PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. This approach increases the confidence in PTES supporting reads. Reads emanating from template-switching events are often characterised by large indels when aligned to the transcriptome. PTESFinder uses additional filters to exclude reads with ambiguous alignments around PTES exon-exon junctions, further increasing confidence in these supporting reads. PTESFinder identifies more PTES structures than other published methods whilst maintaining high specificity. -
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Seqping
Gene Prediction Pipeline for Plant Genomes
Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager. You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided. If you have questions or concerns, please don't hesitate to reach out. Thanks! -
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ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.
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Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. Please visit the Cloudomics, project for cloud-based resources: https://sourceforge.net/projects/cloudomics-for-aws/ -
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CoDeCZ
Derive copy number status from targeted sequencing data
CoDeCZ derives copy number state from targeted sequencing data on gene or exon level. Results are NOT true copy number however, but they are semi-quantitative: It uses the modified z-score to calculate deviation in normalized coverage per specified region. The higher the Z-score, the higher the copy number. The final z-score depends on the quality of the data and the makeup of the reference pool. -
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ExonFinder
A pipeline to extract novel cassette exons/retained-introns
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat. -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
