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Creating my own dynamic badges with github gist endpoint

Introduction Nowadays I’m developing a collection of snakemake pipelines, with automatic assessment of reproducibility of each pipeline via travis CI. To monitor the live status of each pipeline, it will be great to make my own badge showing whether the pipeline is reproducible. For that, I decided to use shields.io to generate my own (dynamic) badge that turns to green if the pipeline is reproducible, or to red if the

Subsampling reads from FASTQ file with awk one-liner

Recently I’ve been entertained by the powerfulness of awk commands in bioinformatics. In this post, I’m going to explain the underlying principles in this awk-extensive BASH one-liners written for random-sampling of FASTQ reads, step-by-step. 1. Random-sampling single-read FASTQ The one-liner is given as below. Note that I fixed some parts in the code which might cause some logical errors. It is pretty illegible, huh? Nevertheless, believe me, the code is