Genome Assembly & Annotation
The draft genome assembly was produced by the Genome Informatics Facility, Office of Biotechnology, Iowa State University. This is an updated version of the GCA_004148225 assembly which uses PacBio long-read sequencing polished with Illumina HiSeq X short-read sequencing reads. Previously deposited Pacbio sequencing (SRX2692203 - SRX2692222) long reads were used with Falcon to generate a new draft assembly which was scaffolded using SNAP read mapper, HiRise and SSPACE-LONGREAD. PILON was used to polish the assembly using the Illumina reads and CCS reads.
The gene predictions were made by the Genome Informatics Facility, Office of Biotechnology, Iowa State University. Gene models were predicted using a MIKADO pipeline. Consensus transcripts from 7 transcriptom assemblies and gene predictions, previously published ESTs, previously published effectors and IsoSeq data were supplied with BRAKER to the pipeline as external evidence.
- Masonbrink RE, Maier TR, Hudson M, Severin A, Baum T. A chromosomal assembly of the soybean cyst nematode genome. Mol Ecol Resour, 2021;21(7):2407-2422
|Iowa State University
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh