Topic cluster

DNA sequencing

Sanger and next-generation sequencing workflows, library quality, read interpretation and what to agree before a run.

sequencing glossary study design sanger ligation ngs amplicon bioinformatics fastq library prep chromatogram coverage fragmentation indexes long reads multiplexing plate maps primers

26 articles

Benchtop sequencing instrument with a teal status light and a flow cell cartridge in a genomics lab

dna sequencing

16S profiling and its taxonomic limits

Judge a 16S profile at the rank the marker supports, and see where copy number, primer bias and species names stop being honest.

8 October 2026 · 10 min read

dna sequencing

A glossary of sequencing terms

Working definitions of read, coverage, depth, MAPQ, Phred, VCF, BAM and the related words, each tied to the mistake that word prevents.

8 October 2026 · 9 min read

dna sequencing

Adapters indexes and barcode hopping

Separate adapter sequence from i5 and i7 indexes, and see why unique dual indexes resist barcode hopping better than one shared index.

8 October 2026 · 8 min read

dna sequencing

Amplicon sequencing for a defined region

Use amplicon sequencing only for the region the primers define, and see why depth, chimeras and primer dropout are not a genome.

8 October 2026 · 10 min read

dna sequencing

Choosing read length and paired ends

Choose read length and paired or single ends from the sequence you must place. Longer short reads help repeats only a little; mates rescue mapping.

8 October 2026 · 7 min read

dna sequencing

Controls and spike-ins for a sequencing lane

Which controls belong on a DNA sequencing lane, why an RNA spike-in does not, and what a failed PhiX-style or known-variant control should stop.

8 October 2026 · 9 min read

dna sequencing

Coverage depth is not the same as accuracy

Separate coverage depth from base accuracy, mapping quality, strand bias and PCR copies so a deep pile of one molecule is not truth.

8 October 2026 · 9 min read

dna sequencing

Data retention and who holds the raw files

Who keeps FASTQ, BAM and VCF, for how long, and what to do before a download link closes. Retention is a custody decision, not a file habit.

8 October 2026 · 8 min read

dna sequencing

From reads to a result a biologist can question

QC, trim, align, deduplicate, call, annotate, filter: the questions a biologist can still ask, and why a PDF gene list is not the data.

8 October 2026 · 8 min read

dna sequencing

GC bias and coverage holes

Extreme GC can look like a deletion. How polymerase and fragmentation leave coverage holes, and how a GC plot differs from a copy-number call.

8 October 2026 · 7 min read

dna sequencing

How short reads and long reads differ

Choose short paired reads or long reads by the repeat, structural variant or homopolymer the experiment actually has to resolve.

8 October 2026 · 9 min read

dna sequencing

Index collisions in multiplexed pools

Same index twice, indexes one edit apart, and sheets written as the reverse complement. How those collisions misassign reads in a multiplexed pool.

8 October 2026 · 8 min read