Jon Palmer

funannotate. Eukaryotic Genome Annotation Pipeline

amptk. AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

funannotate2. Eukaryotic genome annotation software.

redmask. Genome assembly soft-masking using Red (REpeat Detector)

gfftk. GFF toolkit

augustus. AUGUSTUS v3.2.1 for installation on Mac OS X

genome_scripts. collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.

buscolite. BUSCOlite: simplified conserved marker gene prediction for genome annotation

helixerlite. simplified prediction using Helixer for genome annotation

gapmm2. gapmm2: gapped alignment using minimap2 (align transcripts to genome)

gene2product. Curated list of gene names and product descriptions that pass NCBI genome submission rules.

funannotate2-addons. Functional annotation of genomics data for funannotate2

annorefine. AnnoRefine: refine gene models using transcriptomics BAM alignments

jaaws. Jon's Awesome Assembly Wrapper Script

mhc_cluster. Scripts to process MHC DRB2 next-gen sequencing data

funannotate-paper. Scripts used in funannotate manuscript