WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Strongyloides stercoralis

BioProject PRJNA930454 | Data Source NIAID | Taxonomy ID 6248

About Strongyloides stercoralis

The nematode Strongyloides stercoralis, or human threadworm, is a wide-spread, minute gastro-intestinal parasite of humans, occurring principally in the tropics and sub-tropics. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body and can be fatal.

There is 1 alternative genome project for Strongyloides stercoralis available in WormBase ParaSite: PRJEB528

Genome Assembly & Annotation


The genome assembly was produced by the Thomas Nutman Lab at the Laboratory of Parasitic Diseases of the National Institute of Allergy and Infectious Diseases (NIAID), using Oxford Nanopore reads followed by a genome assembly pipeline including Flye 2.8.1 with a minimum overlap allowance of 2500bp, Necat v. December-2021; Smart Denovo v. December-2021; Canu v. December-2021. Following assembly, no polishing occurred as this is built into Flye.

This genome replaced the previous S. stercoralis GCA_000947215 genome as of WormBase ParaSite release 19.


The genes were annotated using an in-house pipeline using both the MAKER pipeline and the FunAnnotate pipeline by the Thomas Nutman Lab at the Laboratory of Parasitic Diseases of the National Institute of Allergy and Infectious Diseases (NIAID).

Three iterations of annotation were run with MAKER. In the first iteration, a gene model was generated using proteins and transcripts taken from the previous S. stercoralis GCA_000947215 genome. The gene model used in the second iteration was taken from the first iteration, and the gene model used in the final iteration was from the second iteration.

For FunAnnotate, gene models were first predicted using the Augustus c_elegans_trsk database, the BUSCO nematoda_odb10 database, and the proteins and transcripts for S. strongyloides taken from the previous S. stercoralis GCA_000947215 genome. After gene prediction, the genome was annotated using the gene model.

Once both annotations were generated, the overlap between the two was then found, and a combined annotation was generated, which used high-quality genes found in either GFF.

Key Publications

  • Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet, 2016;48(3):299-307

Assembly Statistics

AssemblyASM2958206v1, GCA_029582065.1
Database VersionWBPS19
Genome Size44,372,495
Data SourceNIAID
Annotation Version2023-10-WormBase

Gene counts

Coding genes11,641
Non coding genes420
Small non coding genes420
Gene transcripts17,607

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