16S rRNA V1-V2 amplicon analysis
Upload V1-V2 amplicon reads amplified with 27F/338R and get ASVs, SILVA v138.2 taxonomy and diversity statistics in a publication-ready report. The V1-V2 insert is about 273 bp, so trimmed read pairs need about 293 bp combined to merge.
V1-V2 primer sequences
| Region | Forward primer | Reverse primer | Insert length | Reads needed to merge |
|---|---|---|---|---|
| V1-V2 | 27FAGAGTTTGATCMTGGCTCAG | 338RGCTGCCTCCCGTAGGAGT | 273 bp | R1 + R2 ≥ 293 bp |
These are the sequences the V1-V2 preset removes with Cutadapt before denoising. If your facility used a variant of these primers, for example with extra degenerate bases, choose Custom primers on upload and paste the exact sequences from your sequencing report.
Read length and merging
DADA2 merges each forward and reverse read into one sequence, which needs at least 20 bp of overlap. With an insert of about 273 bp, the truncated reads must together reach about 293 bp.
2×250 bp or 2×300 bp. 2×150 bp is too short once primers are removed.
The pipeline starts from default truncation of 260 bp (R1) and 200 bp (R2), then adapts them to the quality profile of your run and re-checks that the pairs can still merge.
When to use V1-V2
Studies that need resolution in the variable V1 region, such as some skin and respiratory work.
- 27F is a near-universal bacterial primer but under-amplifies some groups, including Bifidobacterium.
Comparing regions? Read V3-V4 vs V4 vs V1-V3: choosing a 16S region.
What the V1-V2 analysis includes
- Primer removal with Cutadapt and quality-adaptive truncation
- DADA2 denoising, read-pair merging and chimera removal
- Taxonomy against SILVA v138.2 with exact-match species assignment where possible
- Alpha diversity, rarefaction, phylogenetic tree and PICRUSt2 (Complete tier)
- Beta diversity, PERMANOVA and ANCOM-BC2 across groups in multi-sample projects
See pricing for what each tier includes.
Other 16S regions
V1-V2 analysis FAQ
What are the V1-V2 16S primer sequences?
The V1-V2 preset uses 27F (AGAGTTTGATCMTGGCTCAG) as the forward primer and 338R (GCTGCCTCCCGTAGGAGT) as the reverse primer. Letters such as N, W, Y and V are IUPAC ambiguity codes; the pipeline matches them against real bases when it looks for and removes the primers.
What read length do I need for V1-V2?
The V1-V2 insert between the primers is about 273 bp. DADA2 needs the trimmed forward and reverse reads to overlap by at least 20 bp, so together they must cover about 293 bp. 2×250 bp or 2×300 bp. 2×150 bp is too short once primers are removed.
What is V1-V2 best used for?
Studies that need resolution in the variable V1 region, such as some skin and respiratory work. 27F is a near-universal bacterial primer but under-amplifies some groups, including Bifidobacterium.
What happens if my V1-V2 reads are too short to merge?
The pipeline checks merge feasibility before denoising. If truncated reads cannot reach 293 bp combined, it first extends truncation within the safe quality range; if that is still not enough, the run stops with an explanation instead of silently discarding most read pairs.
Analyze your V1-V2 16S data
Your first 3 analyses are free, with no credit card. Upload FASTQ files and get a publication-ready report, processed and stored in Canada.