Personal code associated with the version 6 update of the Chlamydomonas reinhardtii reference genome
The wider project was a collaboration between several researchers. Genome sequencing, assembly and annotation was performed in collaboration with JGI and general details are provided on Phytozome: https://phytozome-next.jgi.doe.gov/info/CreinhardtiiCC_4532_v6_1
assembly_scaffolding: scaffolding pipeline for preliminary CC-4532 and CC-503 PacBio contigs
repeat_annotation: repeat annotation pipeline
gene_annotation: post-processing of preliminary gene models (coding potential, TE genes, etc.)
MUM&CO: pipeline for structural mutation detection
Cactus_WGA: whole-genome alignment pipeline
H3K4me3_validation: pipeline for gene model validation via H3K4me3