Software and supporting material for: "Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification".

The software is a pipeline for mitochondrial protein annotation in mixed bulk samples. The pipeline annotates mitochondrial genes using homolog prediction with TBLASTN based on known complete mitochondrial genomes from GenBank RefSeq. The BLAST results were then used to determine gene ontology (e.g., mRNA and coding sequence regions) using Genewise. Annotation results include gff format annotation file, DNA and protein sequences of annotated genes. Compared to other mitochondrial annotation pipelines, the MT_annotation_BGI pipeline is easier to run a batch of annotation tasks with high speed and precision. For additional methodological details see the published paper using an example of bulk insect data suitable for running on this pipeline (see dataset here: doi:10.5524/100045).