ArticleScientific reports2015
SeqMule: automated pipeline for analysis of human exome/genome sequencing data.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 80 citations in OpenAlex.
- GATES: A Lightweight Tool Automating Pathogenic Variant Discovery From Raw Whole-Exome Sequencing Data.Cancer informatics · 2026Article
- MOLGENIS VIP: an end-to-end DNA variant interpretation pipeline for research and diagnostics configurable to support rapid implementation of new methods.NAR genomics and bioinformatics · 2025Article
- Whole-exome sequencing to identify causative variants in juvenile sudden cardiac death.Human genomics · 2024Article
- Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer.Nature communications · 2024Article
- Article
- Contribution of uniparental disomy to fetal growth restriction: a whole-exome sequencing series in a prenatal setting.Scientific reports · 2024Article
- Kuura-An automated workflow for analyzing WES and WGS data.PloS one · 2024Article
- Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data.G3 (Bethesda, Md.) · 2023Article
- Innovative Approach to Isolate and Characterize Glioblastoma Circulating Tumor Cells and Correlation with Tumor Mutational Status.International journal of molecular sciences · 2023Article
- Identification of New Potential Prognostic and Predictive Markers in High-Grade Osteosarcoma Using Whole Exome Sequencing.International journal of molecular sciences · 2023Article
- Variant of the catalytic cysteine of UFSP2 leads to spondyloepimetaphyseal dysplasia type Di Rocco.Bone reports · 2023Article
- Resources and tools for rare disease variant interpretation.Frontiers in molecular biosciences · 2023Review
- Article
- Phenotypic Heterogeneity amongBiomedicines · 2022Article
- Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens.PloS one · 2022Article
- JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping.FEBS open bio · 2021Article
- C2orf69 mutations disrupt mitochondrial function and cause a multisystem human disorder with recurring autoinflammation.The Journal of clinical investigation · 2021Article
- iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data.Briefings in bioinformatics · 2021Article
- DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation.Frontiers in oncology · 2021Article
- Loss of supervillin causes myopathy with myofibrillar disorganization and autophagic vacuoles.Brain : a journal of neurology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.
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Registered trials
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.