SeqMule protocols

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SeqMule specifications

Information


Unique identifier OMICS_11956
Name SeqMule
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Single-end or paired-end
Input format FASTQ or BAM
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Kai Wang <>

Publication for SeqMule

SeqMule in pipeline

2017
PMCID: 5655208
PMID: 29113313
DOI: 10.18632/oncotarget.19010

[…] of target regions was 121.7x., the raw data generated from illumina nextseq550 were converted using bcl2tofastq tools provided by illumina. the data analysis of exomes was performed by using the seqmule pipeline1. the final variant call format files (vcfs) were uploaded on the variantstudio illumina (illumina san diego, ca, usa) software to perform annotation and filtration steps. […]


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SeqMule in publications

 (4)
PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] medicine., wes data analysis pipelines integrate computational tools and methods described in the previous sections in a single analysis workflow. here, we review three recent sequencing pipelines seqmule [], fastq2vcf [], and impact [] that assimilate some of the tools described in previous sections., seqmule stands out in part due to the use of five alignment tools (bwa, bowtie 1 and 2, […]

PMCID: 4931320
PMID: 27356984
DOI: 10.1038/ncomms12065

[…] sequencing data, long-read sequencing data and bionano mapping data were performed by the cnvnator, local assembly and irysview software, respectively. snp and indel calling were performed by the seqmule software, which integrates bwa-mem for alignment and gatk/freebayes/samtools for variant calling. comparative analysis of genome assembly was performed by the mummer and the lastz, together […]

PMCID: 4267425
PMID: 25466957
DOI: 10.1186/s12920-014-0066-9

[…] were used for raw data processing and fastq file generation. in total, we obtained ~70 million reads per sample., for bioinformatics analysis of the fastq data from exome sequencing, we used seqmule (http://seqmule.usc.edu), which is an automated pipeline to execute multiple alignment algorithms and multiple variant calling software tools. briefly, sequencing data was evaluated […]

PMCID: 4042683
PMID: 24917883
DOI: 10.3389/fgene.2014.00163

[…] indel was selected using variantannotator in the gatk toolkit (mckenna et al., ; depristo et al., ). the presence and absence the snps and indels sites across different species was checked using the seqmule pipeline (http://seqmule.usc.edu)., sv was detected with pindel (version 0.2.5a1) with default parameters. as quality control, we first detected svs using the mapping result of tilapia reads […]


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SeqMule institution(s)
Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; School of Forestry and Environment, Nanjing Forestry University, Nanjing, Jiangsu, China Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY, USA; Utah Foundation for Biomedical Research, 150 S 100 W, Provo, UT, USA; Department of Psychiatry & Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
SeqMule funding source(s)
This work was supported by National Institute of Health grant HG006465.

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