Posted on Thu 22 August 2019 in commentary • Tagged with bioinformatics, python, workflows
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 …
Posted on Mon 19 August 2019 in how-to • Tagged with bioinformatics, python, workflows, snakemake
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 …
Posted on Wed 17 July 2019 in how-to • Tagged with bioinformatics, data-science, r, python, big-data
Working with large amounts of tabular data is a daily occurance for both bioinformaticians and data scientists. There's a lot the two groups can learn from each other (great future post material). However, I recently ran into a situation that I was sure had to be relatively common. Apparently it …