From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample. Results have been compared between them and against the NIST Genome in a Bottle (GIAB) variants reference dataset. We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome. SNV, and especially InDel, detection is less reliable in 20% of the genome, and almost unfeasible in the remaining 10%. These findings will aid in choosing the appropriate tools bearing in mind objectives, workload, and computing infrastructure available.
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Steve
S
Laurie
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Marcos
M
Fernandez-Callejo
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Santiago
S
Marco-Sola
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Jean-Remi
JR
Trotta
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Jordi
J
Camps
Universitat Autònoma de Barcelona, Bellaterra, Spain.
Alejandro
A
Chacón
Universitat Autònoma de Barcelona, Bellaterra, Spain.
Antonio
A
Espinosa
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Marta
M
Gut
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Ivo
I
Gut
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Simon
S
Heath
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Sergi
S
Beltran
D019295:Computational Biology / Q000379:methods*; D059472:Exome; D014644:Genetic Variation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
NA12878; NGS; alignment; benchmark; bioinformatics; computing speed; variant calling; whole exome sequencing; whole genome sequencing