Repositories list

• gene_rename_workflow

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

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• wi-gatk

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

  Nextflow

  •33 forks•11 star•66 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• geneAnno-nf

  Public
  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 cont…

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• CB_PopGen_HDR_MS

  Public
  scripts, figures, and tables for C. briggsae PopGen and HDR manuscript

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• nemascan-sims-nf

  Public
  Nextflow workflow for running GWA simulations

  R

  •00 forks•00 stars•99 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• Ce_geneAnno-sh

  Public
  This is a repository for storing all scripts related to genome assembly, gene annotation, SV calling, GFF/FA file manipulation, functional enrichment analysis, …

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 20, 2026Jul 20, 2026

• andersenlab.github.io

  Public
  Andersen Lab Website

  HTML

  •

  MIT License

  •33 forks•22 stars•00 issues•22 pull requests•Updated Jul 20, 2026Jul 20, 2026

• cv

  Public
  Andersen Curriculum Vitae

  11 fork•00 stars•00 issues•00 pull requests•Updated Jul 19, 2026Jul 19, 2026

• Ct_pop_gen_project

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• nemascan-nf

  Public
  An updated NemaScan nextflow workflow for version 26+

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• NemaSize-nf

  Public
  Nextflow

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• NemaSize

  Public
  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• easyXpress

  Public
  easyXpress is an R package for the analysis and visualization of high-throughput image-based nematode data

  HTML

  •

  MIT License

  •22 forks•33 stars•1111 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• fq-processing-nf

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

  Nextflow

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2026Jul 9, 2026

• CAENDR

  Public
  HTML

  •

  MIT License

  •33 forks•44 stars•00 issues•99 pull requests•Updated Jul 2, 2026Jul 2, 2026

• gtcheck-nf

  Public
  Nextflow workflow for checking sample variants against known variants to verify identity

  Nextflow

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2026Jul 2, 2026

• Ce_pangenome_MS

  Public
  Scripts, data, figures, and tables for the C. elegans pangenome manuscript

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 1, 2026Jul 1, 2026

• assembly-nf

  Public
  Nextflow pipeline for hifiasm de novo assembly and sequencing quality control

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 27, 2026Jun 27, 2026

• CGC2_genome_MS

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 8, 2026Jun 8, 2026

• NemaScan

  Public
  GWA Mapping and Simulation with C. elegans, C. tropicalis, and C. briggsae

  R

  •33 forks•44 stars•1111 issues•00 pull requests•Updated Jun 2, 2026Jun 2, 2026

• ce_cb_ct_betatubulin

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• 2026_counting_broodsize_images_YOLO

  Public
  Scripts used to count number of animals on a 6 cm NGMA plate using Tau Scientific developed YOLO platform

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2026May 27, 2026

• alignment-nf

  Public
  A nextflow pipeline for genome sequences alignment

  nextflowcelegans

  nextflowcelegans

  Nextflow

  •

  MIT License

  •00 forks•11 star•11 issue•00 pull requests•Updated May 22, 2026May 22, 2026

• VCF-kit

  Public
  VCF-kit: Assorted utilities for the variant call format

  pythonvcf

  pythonvcf

  Python

  •

  MIT License

  •2727 forks•137137 stars•1919 issues•00 pull requests•Updated May 22, 2026May 22, 2026

• annotation-nf

  Public
  Annotate VCF with snpeff and bcsq

  Perl

  •33 forks•22 stars•44 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• HDR_haplotypePlotter

  Public
  R script that generates gene-level visualization of hyper-divergent haplotypes using G2G alignments

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• vertTrans_microbe_discovery

  Public
  C. elegans pathogen discovery through taxonomic classification from unaligned wild strains reads

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• caenorhabditis_colors

  Public
  Color codes for Caenorhabditis species and strains

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 8, 2026Mar 8, 2026

• trim-fq-nf

  Public
  Nextflow

  •

  MIT License

  •11 fork•00 stars•22 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• migrate-sims-to-db-nf

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026