Resources

Tools, pipelines and databases from my work.

• OikoBrowser oikobrowser.com

  Genome browser for Oikopleura dioica built on JBrowse 2, with BLAST search across the assemblies.

• CAGEscan Nextflow pipeline github.com/johannesnicolaus/cagescan_nextflow

  Nextflow pipeline for processing CAGEscan and paired-end CAGE data.

• Improved genome annotation of Oikopleura dioica github.com/oist/Oikopleuradioica_genomeannotation

  Genome annotation of Oikopleura dioica populations from different geographical locations.

• rRNAscan github.com/oist/luscombeu_rrnascan

  Nextflow pipeline to scan sequencing data for rRNA reads and extract them.

• NANOPlasty and nanoplasty-nf github.com/johannesnicolaus/nanoplasty-nf

  NANOPlasty is a de novo assembler for short circular genomes, such as mitochondria and plastids, from long reads (ONT/PacBio). nanoplasty-nf runs it as an nf-core-style Nextflow pipeline.

  NANOPlasty nanoplasty-nf

• egapx_nf github.com/johannesnicolaus/egapx_nf

  Pipeline that prepares RNA-seq data for NCBI’s EGAPx genome annotation pipeline from nf-core-style samplesheets, and runs downstream QC.