Alignment
Avadis NGS provides support for aligning reads to a genome for small RNA reads, DNA reads (for ChIP-Seq and DNA-Seq applications), and RNA reads (spliced and unspliced reads) from sequencing platforms like Illumina, Ion Torrent, ABI, 454 (Roche), and Pac Bio. The aligner, called COBWeb, uses a new proprietary algorithm based on the Burrows Wheeler Transform. Other alignment algorithms are often limited to either a specific class of reads or alignment characteristics. COBWeb, however, has been optimized to handle both short reads and long reads, allows an arbitrary number of gaps and mismatches, and handles both single and paired end reads.
Watch a recording of our webinar on Alignment with COBWeb!
Pre-alignment QC
Inspect raw read quality using pre-alignment QC plots, such as base and read level quality distributions, quality and composition by position.
Customizable Alignment Options
Use options for trimming adaptors and low quality bases, as well as for screening reads against standard screening databases.
Post-alignment QC
Check aligned reads for alignment accuracy using post-alignment QC plots and move on seamlessly to the applicable analysis workflow.
Workflow Specific Alignment Options
Align against the whole genome or target regions for DNA-Seq, align against known transcriptome for RNA-Seq and/or genome for novel discovery, remove adapters for small RNA-Seq.
