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 1,000 sequences free or 50,000 rows with Tool Membership, 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.
Use this batch sequence QC page for pool-scale validation before synthesis submission. The QC guides can help set thresholds and interpret vendor or NGS reports; this tool performs the actual sequence screening.
If the order is a pool, run this QC before vendor comparison or order-file formatting. Vendor shortlist and file conversion decisions are cleaner after GC, homopolymer, length, Tm, low-complexity, and structure-risk rows are flagged.
Typical input includes a FASTA list, one sequence per line, or a vendor-prep CSV/TSV with a sequence column. Review GC outside target range, long homopolymers, Tm outliers, low complexity, length drift, and structure risk before moving passing rows into vendor-specific order formatting.