SeqMule: automated pipeline for analysis of human exome/genome sequencing data

Guo, Y., Ding, X., Shen, Y., Lyon, G. J., Wang, K. (September 2015) SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep, 5. p. 14283. ISSN 2045-2322 (Electronic)2045-2322 (Linking)

[thumbnail of Paper]
PDF (Paper)
Lyon Sci Reports 2015.pdf - Published Version

Download (967kB) | Preview
DOI: 10.1038/srep14283


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

Item Type: Paper
Subjects: bioinformatics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > computers > computer software
Investigative techniques and equipment > assays > next generation sequencing
Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL labs > Lyon lab
Stanley Institute for Cognitive Genomics
Depositing User: Matt Covey
Date: 18 September 2015
Date Deposited: 25 Sep 2015 14:40
Last Modified: 09 Nov 2017 21:35
PMCID: PMC4585643
Related URLs:

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving