Ramanauskas, K. and Igić, B. 2023. kakapo: easy extraction and annotation of genes from raw RNA-seq reads. PeerJ 15:e16456 (13pp). DOI: 10.7717/peerj.16456
We added a Wiki with detailed explanations, including step-by-step, multi-platform installation instructions.
Studies in many fields within the life sciences increasingly rely on RNA sequencing (RNA-seq) data. As a result, RNA-seq datasets deposited to the NCBI Sequence Read Archive (SRA) are proliferating. In addition to serving as an archive for the original studies, these datasets present an opportunity for novel research.
kakapo is a pipeline that allows users to extract and assemble a specified gene or a protein family from any number of SRA accessions (or their own RNA-seq data). kakapo identifies open reading frames in the assembled transcripts and annotates them using InterProScan. Additionally, raw reads can be filtered for ribosomal, plastid, and mitochondrial reads or reads belonging to non-target organisms (viral, bacterial, etc.)
kakapo can be flexibly employed to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics.
A 12-minute overview of kakapo from my Botany 2020 conference talk: https://youtu.be/2D04DQlV6CA