Bioinformatics insights
Eight Unix habits that save bioinformaticians hours
Practical command-line patterns for inspecting huge files, parallelizing QC, protecting long-running jobs, and preserving error logs.
Inspect before you load
Use streaming tools such as head, tail, zcat, and less to inspect large text or compressed files without opening the entire dataset in memory. This simple habit is especially useful for FASTQ, VCF, GTF, and count matrices.
Count and sort with purpose
Combining cut, sort, uniq, and wc provides fast answers about identifiers, annotations, and category frequencies. Always confirm delimiters and header lines before interpreting results.
Parallelize repeatable work
Independent per-sample tasks—quality control, trimming, alignment checks—can often run concurrently. Match concurrency to available CPU and memory, and record the exact command used.
Keep jobs alive and logs complete
Run long tasks in tmux, screen, or a scheduler such as SLURM. Redirect standard error to timestamped logs so a failure remains diagnosable after the terminal session ends.