Program, Pipeline Name or Method Name

BRAKER, AUGUSTUS

Program, Pipeline or Method version

2015

Source Name

Seriola dorsalis annotation version 1 in gff3 format

Time Executed

Sept. 9, 2016, midnight

Category

Genes

Description

BRAKER (Hoff et al. 2015) was used to annotate the genome using raw RNA-Seq data. BRAKER pipeline uses GeneMark-ET (Lomsadze et al. 2014) to perform unsupervised training using a genome file and the RNA-Seq data. After training, GeneMark-ET creates an ab initio gene set. Those gene structures that have support by RNA-Seq alignments in all introns are selected for automated training of AUGUSTUS (Stanke & Waack 2003). After training, AUGUSTUS predicts genes in the input genome file using spliced alignment information from RNA-Seq as extrinsic evidence. Using raw RNAseq data helps to accurately identify exon/intron boundaries better than methods that rely on assembled transcripts.

File

sedor_v1_sorted.gff3.gz

Index

sedor_v1_sorted.gff3.gz.tbi