Novoalign supports adapter striping of both Solexa/Illumina 3′ adapters and 5′ adapters that may have been added in a PCR step.
- 3' Adapter Stripping - Single End Reads
- Paired End Short Fragment Detection
- 5' PCR Adapter Stripping
When DNA fragments are shorter than the read length the reads will extend into the Solexa/Illumina 3′ adapter sequence. This situation can occur with miRNA where you have targeted very short fragments and can also occur in a normal run where some short fragments may remain in the sample.
With Paired-End the presence of adapter corresponds with DNA fragments or inserts that are shorter than the read length so that the read extends into the adapter sequence as per single end reads. However for paired end the two reads, once trimmed of adapter should also be complementary as they are the same fragment read in both directions. Novoalign can align two reads of a pair against each other to detect short fragments with adapter and then trim the adapter sequence.
is required with some protocols such as Nimblegen Sequence Capture arrays where fragments have undergone PCR amplification with proprietary adapters before the addition of the Illumina adapters.
