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

kakapo (kakapo) 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 global assembly of entire transcriptomes or metatranscriptomes. 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 for targeted assembly, 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 GenBank's single-gene databases and help assemble datasets for a variety of phylogenetic analyses.

Automated summary

kakapo is a Python-based pipeline that allows users to extract and assemble specified genes or gene families. It can flexibly process original RNA-seq reads or GenBank SRA accession inputs without the need for global assembly. The pipeline identifies open reading frames in the gene transcripts and annotates them, and it can also filter out reads from non-target organisms.