NGSUtils protocols

NGSUtils specifications


Unique identifier OMICS_02104
Name NGSUtils
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTQ, BED, BAM
Output format FASTQ, BED, BAM
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS
Programming languages Python
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Marcus R. Breese <>

Publication for NGSUtils

NGSUtils IN pipelines

PMCID: 4931717
PMID: 27386501
DOI: 10.1002/acn3.322

[…] removed from the analysis. the number of all possible bases (a, t, c, g) for each position were counted using gatk's “depthofcoverage” tool (bases with low quality [q < 30] were discounted) and ngsutils's (v0.5.7) “basecall” tool was used to count the number of insertions and deletions at each position. the variants excluded from the analysis were 333 variants with a minor allele frequency […]

PMCID: 5011741
PMID: 27597120
DOI: 10.1038/srep32731

[…] by bowtie v1.0.053 to gencode lncrna reference (release 17) and ucsc grch37/hg19 knowngene reference, respectively, for lncrna and mrna annotations. transcript abundances were quantified using ngsutils54. samples were further filtered based on percentage of genes detected (less than 50%) and percentage of reads mapped to the reference (less than 25%). extreme outliers […]

PMCID: 4378619
PMID: 25680078
DOI: 10.1371/journal.pgen.1004999

[…] the reads were mapped to the reference genome saccer3 only based on the facts that in yeast there is some splicing but most genes do not have introns. read counts were calculated using bamutils from ngsutils [82]. differential gene expression was analyzed using edger which calculated all normalized read counts, p-values, and fdr values listed in s1 table [83]. all raw and processed files […]

PMCID: 4144887
PMID: 25157846
DOI: 10.1371/journal.pone.0105644

[…] best hits were reported with only one mapping location. on average, 95% of the total reads were mappable. the total number of reads corresponding to each annotated region was determined with ngsutils software (version 0.5.5) [46]. differential gene expression analysis across different strains was conducted using the bioconductor package edger [47]. batch effects among biological […]

PMCID: 4183418
PMID: 25275310
DOI: 10.1371/journal.pgen.1004648

[…] on an illumina hiseq. the resulting reads were demultiplexed and aligned to the human genome (hg19) using tophat v2.0.10 [68]. read counts for each gene in the refseq annotation were obtained using ngsutils [69] so as to allow comparison to the rna-seq data from the other 7 primary hepatocytes treated with and without rifampin and sequenced with solid as described in [37]. analysis […]

NGSUtils institution(s)
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
NGSUtils funding source(s)
National Institutes of Health (AA017941, CA113001, GM088076); Indiana Biobank

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