Скачать или смотреть Quality Control: NCGAS Transcriptome Assembly, Annotation, and Analysis Workshop

From the National Center for Genome Analysis Support (NCGAS) workshop on high performance computing (HPC) usage and transcriptome assembly, annotation and analysis.

Presented by Layla Freeborn, Bioinformatics Analysist, NCGAS. Filmed July 20, 2021.

ABOUT THE WORKSHOP
The workshop consists of discussions, lectures, and hands-on tutorials/activities to cover topics important to getting started constructing and analyzing transcriptomes. While the focus is largely on de novo assembly, genome-guided transcriptome assembly and analysis is discussed, and demo code is provided. Material covers both the availability and use of HPC resources, alongside the task of assembling a new transcriptome, in order to provide a more comprehensive preparation for this and future bioinformatic tasks. The main case study will consist of using four separate assemblers (Trinity, SOAP de novo, Velvet Oases, and TransABySS), with multiple kmers, to be combined and curated with Evigenes. This combined assembly with multiple parameters is considered much more robust than simply using one assembler, and the NCGAS pipeline streamlines the process and allows for customization if desired. Downstream analyses such as differential expression, generating KEGG pathway images, and annotation using Trinotate will also be discussed. While material will make heavy use of XSEDE and IU machines, the material is transferable to any cluster. For more information about this online/on-demand workshop, visit https://go.iu.edu/29rf .

The National Center for Genome Analysis Support (NCGAS) is a management group in Research Technologies (RT), a division of University Information Technology Services. RT and NCGAS are centers in the Pervasive Technology Institute at Indiana University.
https://ncgas.org