Analyze up to 10,000 sequences simultaneously for quality issues, including GC content, Tm deviation, secondary structures, homopolymers, and low complexity regions. Export flagged sequences for redesign. For step-by-step workflows, follow our pre-order oligo pool QC workflow or check the User Guide for best practices.
Upload a FASTA file or paste sequences to begin quality control analysis.
Batch Sequence QC is the systematic analysis of all oligonucleotide sequences in a pool or library before placing a synthesis order. It identifies sequences that are likely to fail during synthesis, have poor functional performance, or introduce bias into downstream experiments. For oligo pools used in CRISPR screens, gene assembly, or mutagenesis libraries, pre-synthesis QC is essential to avoid costly redesign cycles.
Our Batch Sequence QC tool analyzes up to 10,000 sequences simultaneously, checking each for: GC content extremes, homopolymer runs (repeated bases like AAAAA), low-complexity regions, Tm outliers, potential secondary structures, and length violations. Each sequence receives a risk score, and flagged sequences are highlighted with specific failure reasons.
The tool generates a downloadable QC report with summary statistics (pool-wide GC distribution, Tm range, flag frequency) and per-sequence details. This report can be shared with synthesis vendors to discuss design modifications or used internally to guide sequence redesign before ordering.
After QC, estimate your pool's expected representation uniformity and dropout rate.
Calculate expected synthesis error rates and full-length percentage for your sequences.
Deep-dive into GC content distribution for individual sequences flagged by Batch QC.
Need a direct next step?
Use support@oligopool.com for bug reports, feature requests, and tool questions. If something looks off, route it through one inbox instead of hunting for separate links.
Continue with the guide, reference, or workflow that matches the next decision in your experiment.