ArticlePloS one2021
Multithreaded variant calling in elPrep 5.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Shock-scattering micro-histotripsy-aided fine needle aspiration for enhanced biomarker profiling and cytopathology.Nature communications · 2026Article
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- Artificial Mutations in the Nuclear Gene Encoding Mitochondrial RNA Polymerase Restore Pollen Fertility in Cytoplasmic Male Sterile Tomato.Plant biotechnology journal · 2026Article
- Shared and Unique Patterns of Genomic Differentiation and Introgression Between Japanese Stickleback Species Across Three Sympatric Sites.Molecular ecology · 2026Article
- Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.Environmental microbiome · 2025Article
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata).Scientific reports · 2024Article
- Genomic diversity of the Japanese wheat core collection and selection of alleles for agronomic traits in the breeding process.Breeding science · 2024Article
- COSAP: Comparative Sequencing Analysis Platform.BMC bioinformatics · 2024Article
- A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.BMC biology · 2023Article
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- DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data.BMC bioinformatics · 2023Article
- Article
- Halvade somatic: Somatic variant calling with Apache Spark.GigaScience · 2022Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK4. This makes elPrep 5 a suitable drop-in replacement for GATK4 when faster execution times are needed.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.