kakapo: Easy extraction and annotation of genes from raw RNA-seq reads

Abstract

kakapo (k[a]k[a]p[o]) is a python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing assembly of entire transcriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of the GenBanks single-gene databases and help assemble datasets for a variety of phylogenetic analyses.