Abstract Detail

Phylogenomics

Ramanauskas, Karolis [1], Igić, Boris [1].

Extract and annotate genes from raw RNA-seq reads: kakapo.

Studies in many fields within 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. Here, we present Kakapo, a pipeline that allows users to extract and assemble a specified gene or 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.) We demonstrate the utility of this pipeline with a case-study: the identification of putative self-incompatibility locus in Schlumbergera truncata (Cactaceae).

Related Links:
kakapo GitHub repository

1 - University of Illinois at Chicago

Keywords:
SRA
RNA-seq
self-incompatibility
gene family evolution
evolution.

Presentation Type: Oral Paper
Session: PHYL4, Phylogenomics IV
Location: Virtual/Virtual
Date: Friday, July 31st, 2020
Time: 4:30 PM
Number: PHYL4007
Abstract ID:865
Candidate for Awards:None