Ten recommendations for creating usable bioinformatics command line software
Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s...Tags: Bioinformatics, Computational Biology, Rules, Server, Software, Tips, Suggestions
3582 days ago
Bioinformatician’s Pocket Reference !!
It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core ...Tags: Bioinformatics, Computational Biology, Pocket, Reference
3582 days ago
Bioinformatics algorithms tutorials
Useful bioinformatics tutorial, such as De Bruijn Graphs for NGS AssemblyAlgorithms for PacBio ReadsSoftware and Hardware Concepts for BioinformaticsFinding us in Homolog.us (Search Algorithms)NGS Genome and RNAseq Assembly - a Hands on PrimerIntroduction to PERL, Python, R and C/C++ for Bioinfo...Tags: Bioinformatics, Computational Biology, NGS, Tutorial, Algorithms, Concept
3566 days ago
Orione – a web-based framework for NGS analysis in microbiology
End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult due t...Tags: Bioinformatics, Computational Biology, NGS, Orione, Microbiology, Visualization
3537 days ago
Integrative Genomics Viewer (IGV) tutorial
The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants. http://www.broadinstitute.org/...Tags: Bioinformatics, Computational Biology, NGS, IGV, Visualization, Tutorial
3548 days ago
COSMOS, our workflow management system for NGS data
COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download fo...Tags: Bioinformatics, Computational Biology, NGS, COSMOS, Python, Workflow
3537 days ago
Tags: Bioinformatics, Computational Biology, Protein, Docking
3521 days ago
Swabs to Genomes: A Comprehensive Workflow
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library pr...Tags: Bioinformatics, Computational Biology, Workflow, Genome, Commands
3519 days ago
Tags: Bioinformatics, Computational Biology, Big data, Analysis, Share, Run, Compute, Free, Arvados, Organise, Store
3477 days ago
Java utilities for Next Generation Sequencing by Pierre Lindenbaum
Java utilities for Bioinformatics https://github.com/lindenb/jvarkitTags: Bioinformatics, Computational Biology, Java, Utilities #Tools #Scripts #Pierre
3482 days ago