The upcoming release of Avadis NGS 1.3 provides support for aligning raw reads to the genome – for small RNA, ChIP-Seq and DNA-Seq experiments. The alignment program integrated with Avadis NGS is a new proprietary algorithm called COBWeb. The name loosely comes from the approach we took to developing the algorithm – a computationally-optimized Burrows Wheeler transform (BWT).
You won’t need to search for other aligners, which are limited to either a specific class of reads or alignment characteristics. COBWeb is designed to handle both short reads and long reads, as well as allow an arbitrary number of gaps and mismatches. Moreover, with an alignment program in the same software as downstream analysis functions, you now have a complete pipeline of sequencing tools – from the time you receive your raw reads till you publish your manuscript!
We will host a webinar in early December when we will provide a more detailed overview of COBWeb, along with comparisons to several existing open source tools for alignment.