A reproducible nextflow to call HDRs in selfing nematodes.

A nextflow pipeline for taking raw sequenced reads (fastqs) and performing trimming, species check, alignment, and genotype checking

This is a nextflow process that predicts gene models in Caenorhabditis de novo assembled genomes using BRAKER3. The input to this process is a TSV/TXT that contains three columns: species, strain, <pathToAssembly>. Column headers of "species", "strain", "asm_path" are required.

This is a repository for storing all scripts related to genome assembly, gene annotation, SV calling, GFF/FA file manipulation, functional enrichment analysis, gene set visualization, and syntelog decompression.

Nextflow pipeline for hifiasm de novo assembly and sequencing quality control

Nextflow pipeline for calling isotype groups

Combine OrthoFinder and Reciprocal Best Blast Hits to annotate gene names across Caenorhabditis species

The new GATK-based pipeline for wild isolate C. elegans strains