FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow

Abstract

Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for proofreading and improving gene structural annotation. Here, we introduce FA-nf, a pipeline implemented in Nextflow, a versatile computational workflow management engine. The pipeline integrates different annotation approaches, such as NCBI BLAST+, DIAMOND, InterProScan, and KEGG. It starts from a protein sequence FASTA file and, optionally, a structural annotation file in GFF format, and produces several files, such as GO assignments, output summaries of the abovementioned programs and final annotation reports. The pipeline can be broken easily into smaller processes for the purpose of parallelization and easily deployed in a Linux computational environment, thanks to software containerization, thus helping to ensure full reproducibility.

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

“…Additional pipelines for extended gene annotation ( 22 ), downstream functional analysis ( 23 ) and phylogenomic analysis ( 24 ) already exist and are being reimplemented as scalable and reproducible workflows using NextFlow ( 25 ) and SnakeMake ( 26 ).…”

Comprehensive RNA-Seq Analysis Pipeline for Non-Model Organisms and Its Application in Schmidtea mediterranea

“…The results of transcriptome analysis can be further input in gene differential expression analysis and gene ontology analysis in R; the relevant tools are listed in Table 1. Compared with the previous RNA-seq pipeline for non-model organisms, FA-nf [4], PipeOne-NM integrates predictions for both novel lncRNAs and circRNAs, retrotranscriptomes, and alternative splicing (Table 2).…”

“…Without functional gene annotations, exploring the function of differentially expressed genes and enriching these genes in certain pathways can be complicated. Some packages have been developed to carry out these functions already, focusing on effectively assembling and annotating genome of non-model organisms [3,4]. With functional annotation of genome and transcriptome, studies of non-model organisms can help shed light on gene expression regulatory networks under different biological contexts [5], thus utilizing some of the key components in order to bring economic or ecological benefits.…”

AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data

“…Considering the growing datasets of genomic and proteomic databases, and the specific genomic features across taxa, combining different computational tools or pipelines to automatically assess gene structural and functional annotation has been widely used ( Danchin et al, 2018 ). Composed of a set of data processing methods connecting inputs and outputs in series, automated pipelines can perform genome annotation by sequence similarity ( Hyatt et al, 2010 ; Steinbiss et al, 2016 ) or functional annotation of proteins ( Gotz et al, 2008 ; Vlasova et al, 2021 ; Törönen and Holm, 2022 ). Nevertheless, only a few genome annotation pipelines use expression experimental data (RNA-Seq or MS/MS) to validate the in silico annotation ( Ghali et al, 2014 ; Sheynkman et al, 2014 ).…”