Computational biology and genomics
The article “A new coronavirus associated with human respiratory disease in China” released the full genome sequence (29,903 nt) of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the paper, meta-transcriptomic sequencing was performed on bronchoalveolar lavage fluid (BALF) from a 41 year old male suffering from a severe respiratory disease. Contigs were assembled using…
Some of you may have noticed the Buy me a coffee link I have on my blog. I have just used all the contributions to help pay for the hosting fees; this blog should be here for another two years (extended up until 2022 April 24). Thank you to everyone who has bought me a…
If you are planning on running some of the GATK workflows locally you will require various reference files, known as the Resource Bundle. Initially I had downloaded the files using FTP but I later realised various files were missing from the FTP server, such as BWA index and scatter files. Only later did I realise…
An approach I like to use when learning a new tool is to get started by trying to run an example and then gradually work out the details. In this post, I’m trying to learn the basics of the Workflow Description Language (WDL) so that I can adapt GATK workflows for my own use. WDL,…
The Australian Bureau of Meteorology provides historical weather data, some of which can be freely downloaded. In this blog post, I will plot the weather data collected at two weather stations in Brisbane: the Brisbane Regional Office weather station (latitude 27.466 degrees south, longitude 153.0270 degrees east, and elevation of 38 metres) with data available…
The Broad Institute have shared their GATK workflows on GitHub, however they are configured to be used with Google Cloud. I was not able to find a lot of information on executing the workflows locally and I only found this tutorial. I ran into problems while trying to follow the tutorial but eventually got it…
Amazon S3 is an affordable resource for storing your data; you pay for what you use. There are four cost components to consider: 1. Storage pricing (how much space you use) 2. Request and data retrieval pricing (number of requests you make) 3. Data transfer and transfer acceleration pricing (how often you transfer the data)…
I will be giving a workshop titled “Reproducible Bioinformatics” at BioC Asia tomorrow. I have been thinking a lot about this topic and my aim for the workshop is to introduce computational tools and demonstrate how they can be used to help promote reproducibility when performing bioinformatic analyses. Ensuring reproducibility shouldn’t be an extra burden…
In this post, I will compare different tools for comparing VCF files. To create a reproducible example, I will make use of Docker and Conda. I highly recommend learning about these tools if you haven’t already; they make it easier to reproduce your work. I have written some notes on Docker and Conda that maybe…
This is an update on my original post Setting up Windows for bioinformatics that I wrote in 2011. I had switched over to the Mac operating system (Mac OS X) for work when my HP laptop was replaced with a MacBook Air sometime in 2012. A few years later, I wiped my Windows installation from…