Producing an assembly is often the end goal of many sequencing projects, and there is a complex landscape of assembly options that we are happy to help you navigate. Advances in long read technology on the Oxford Nanopore and PacBio platforms have made many traditional assembly methods outdated or obsolete. Meanwhile, Illumina’s per-base value has continued to improve, and the economic accessibility of Illumina has provided a plethora of high-throughput, high-quality data.
SeqCenter specializes in leveraging both read length and read accuracy to generate high quality collapsed de novo draft assemblies, with peer-reviewed, open-source software. Below are four types of automated draft assembly services we offer, with specific requirements and example methods detailing the software used for each pipeline. As with all bioinformatic analyses, SeqCenter recommends that customers ensure that a given workflow is appropriate for their organism and sample type, and to validate all results. All draft genomes should be reviewed and adjusted according to organism-specific best practices before submission or use.
PacBio Long Read Assemblies
The quality and read length of PacBio data is unmatched in the current genomic climate. We observe an average read length between 15-18kb in our PacBio datasets with about 98% of the dataset exceeding Q30 quality scores. These long, highly accurate reads generate the best assemblies that we observe at SeqCenter, as they can easily assemble through complex and repeat-rich genomic regions.
The on-instrument base detection can also capture raw methylation kinetics, which are retained in the generated BAM files. Upon assembly, we can map the raw kinetic data to the generated assembly to report genomic locations that are likely 4mC or 6mA methylation sites, relative to the final assembly.
We routinely utilize this pipeline for bacterial and fungal samples to create beautiful de novo genome assemblies and annotations. For additional information on PacBio collapsed assemblies for higher-order Eukaryotes, please contact us. Example of methods documents can be found here for prokaryotic samples and here for eukaryotic samples, detailing the software that will be used.