My day doesn’t start with a microscope. It starts with a terminal. Usually, I’m staring at a 50GB FASTQ file that decided to corrupt itself at 2:00 AM.
I found 10,000 variants. The lab expected 5. Did I mis-call indels? Is there a batch effect? Did someone accidentally use the mouse reference genome again? (It happened once. Once.)
bwa mem genome.fa sample_R1.fastq sample_R2.fastq > aligned.sam samtools sort -@8 aligned.sam -o sorted.bam freebayes -f genome.fa sorted.bam > variants.vcf Then I wait. This is when I practice patience. And refresh my email 47 times. david bioinfo
Why ‘rm -rf’ is scarier than a pipette tip, and other truths of digital biology. Introduction: Hello, World (of Omics)
The first rule of : Always check your checksums. My day doesn’t start with a microscope
As David the bioinformatician, my real value isn’t typing fast. It’s knowing when a result is biologically plausible vs. computationally correct but nonsense .
Hi! I’m David. Ask me what I do, and you’ll get a different answer depending on the day. I found 10,000 variants
The hardest part of my job isn’t the code—it’s the interpretation .