Resources

CGC2 – gap-free telomere-to-telomere reference for AF16 (2026). No gaps, no unplaced sequence, chromosome-level contiguity, with protein-coding annotations and a liftover of 108 validated indel variants. O’Connor et al. (2026) G3 16(8):jkag158
Chromosome-level assemblies for QX1410 and VX34 – QX1410 (closely related to AF16) and VX34 (a divergent Chinese isolate), with 99 recombinant inbred lines genotyped at 2,981 SNP markers. Stevens et al. (2022) Genome Biology and Evolution
C. briggsae on WormBase – gene pages, genome browser, and the CB4 assembly. Species page · JBrowse · Downloads
C. briggsae on WormBase ParaSite – browse and download
NCBI BioProject PRJNA10731 – sequence data and assemblies
Caenorhabditis Genomes Project – genome assemblies and annotations across the genus, plus BLAST and gene trees. Essential for comparative work. caenorhabditis.org
Original genome sequence – Stein et al. (2003); chromosome assembly – Hillier et al. (2007)
Improved C. briggsae assembly and the C. nigoni genome – Ren et al. (2018), summarised here

Caenorhabditis Genetics Center (CGC) – Stock centre. cgc.umn.edu · search strains · wild isolates
Mutant and transgenic strains (Gupta lab) – strain database. See also Bi et al. (2015) PLoS Genetics for GFP-integrated transgenic lines.
Recombinant inbred lines – AF16 × HK104: Ross et al. (2011) PLoS Genetics. QX1410 × VX34 (99 lines): Stevens et al. (2022)
Wild isolates – at least 63 from around the world. Cutter et al. (2006) Genetics
MosI transposon mutant screen (M.-A. Félix) – details

CaeNDR – the Caenorhabditis Natural Diversity Resource. Covers C. elegans, C. briggsae and C. tropicalis: wild strain collection, whole-genome sequence, annotated variants, and tools for genome-wide association mapping. This supersedes the former CeNDR. caendr.org
Cite: Crombie et al. (2023) Nucleic Acids Research

Linkage maps – polymorphism-based and phenotypic marker-based, with SNP and indel tables. See Genetics & Genomics.
Gene mapping toolkit – Koboldt et al. (2010) BMC Genomics 11:236
Polymorphism lists (SNPs and indels, text files)
Raw sequence reads – HK104, VT847, HK105, PB800

Community-curated gene models – a community effort correcting and improving C. briggsae gene structures. Novel and improved C. briggsae gene models (2023)
TEC-RED 5′ end analysis – new exons, paralogs, and conserved and novel operons. Jhaveri et al. (2022) G3
Process-specific gene sets (vulva, dauer, sex determination, body morphology) – see Genetics & Genomics. These sets are historical and not maintained.

Kept for reference because they are cited in older literature. These resources are no longer maintained, and several are no longer reachable.

Original briggsae.org site – largely superseded, but still hosts several data files linked above
Washington University St. Louis SNP map – locally mirrored
C. briggsae fosmid genomic DNA library (MPI-CBG TransgeneOmics) – no server response when last checked
nematode.net (Washington University, St. Louis) – no server response when last checked
NEMBASE – was listed via the Pittsburgh OBRC directory, which was retired in May 2026
Leon Avery’s C. elegans server – shut down
C. briggsae Ensembl FTP trace server – obsolete
RPCI-94 BAC genomic clones (CHORI) – no longer distributed
Worm meeting abstracts – obsolete

Know of a resource that should be listed here, or spot a link that is broken? Please leave a comment or get in touch. Corrections are very welcome.

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