TLDR - Check out this github repo for a (still really wordy) example: polyglot_jupyter_example

If you're anything like me, and there are probably tens of you out there, you enjoy working in multiple programming languages for your bioinformatics/data science work. Perhaps you love the tidyverse R ecosystem for data manipulation …

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TLDR - Check out this github repo for the full example: https://github.com/groverj3/minimal_nextflow_samplesheet_example

I recently wrote an article regarding some of my opinions on bioinformatics workflow design. I've written workflows in several languages over the years, but at this point it seems that Nextflow has become something of …

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How do you communicate results of an analysis? What tools do you use? Scientists that work in the wet lab are accustomed to firing up excel or some instrument-specific software and working with their own data. For genomics or other types of experiments in biology that result in large datasets …

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Since I was in grad school I've been writing bioinformatics workflows. Usually to process NGS data. The concept of a workflow is simple, and not limited to the domain of bioinformatics. However, a workflow (aka "pipeline") used to analyze data from next generation sequencing (again, will it ever be "current …

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One of the, if not the, most common downstream analysis task I'm asked to perform on RNAseq data is to generate the venerable "Volcano Plot." These are kind of the bioinformatics equivalent of saying "Hey! Look how much data I have!" Regardless, they are a pretty good way to quickly …

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Back in 2019, the halcyon days of yore, near the end of my time in graduate school I wrote a well-intentioned article about software management for multi-user linux systems (here). This original article was written based on my experiences as the de-facto sysadmin of our lab's bioinformatics server. I am …

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I started this github site as a place to expand my professional reach by posting my random musings on bioinformatics, Linux, data science, and etc. I made a few reasonably cogent posts, but then life got in the way! It's been a really busy time, a very eventful year. I'm …

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In contrast to the zen of python there are actually many ways to handle sequence data in Python. There are several packages on PyPI that provide parsers for sequence formats like .fastq and .fasta. I've never bothered with these, including the oft-used Biopython. I vaguely remembered Biopython being slower than …

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Over the past few years the use of workflow managers in genomics and bioinformatics has grown greatly. This is a great thing for the field and adds to our ability to perform reproducible analyses, especially for pipelines with many steps. These are common in bioinformatics, but prior to the use …

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Bioinformatic analyses often require lengthy workflows or pipleines, where the output of program A feeds into program B, and so on. These programs may also not output their results in a format which is convenient to use in the subsequent steps, requiring writing a conversion script, or piping its output …

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