NGSUtils protocols

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NGSUtils specifications

Information


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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Maintainer


  • person_outline Marcus R. Breese <>

Publication for NGSUtils

NGSUtils in pipelines

 (9)
2016
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 […]

2016
PMCID: 5011741
PMID: 27597120
DOI: 10.1038/srep32731

[…] mapped by bowtie v1.0.0 to gencode lncrna reference (release 17) and ucsc grch37/hg19 knowngene reference, respectively, for lncrna and mrna annotations. transcript abundances were quantified using ngsutils. 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 were further identified […]

2016
PMCID: 5190036
PMID: 27259276
DOI: 10.18632/oncotarget.9779

[…] genome mm9 and a splice-junction library, respectively; the genomic and splice-junction library mapping were merged at the end. the gene based expression levels were calculated using bamutils from ngsutils based on the refseq gene annotation of mm9 []. differential expression of genes across different treatments was determined with edger []. statistically significant differentially expressed […]

2015
PMCID: 4354993
PMID: 25608970
DOI: 10.1186/s13059-015-0580-x

[…] aligned to the arabidopsis genome (tair10) using bowtie2 (parameters: --local -k 6). gene expression values were calculated by summing the number of reads aligning to any annotated gene exon, using ngsutils. reads aligning to more than one genomic location were counted as partial read. genes with coverage of less than 200 bp were removed from downstream analysis. number of reads per gene […]

2015
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 []. differential gene expression was analyzed using edger which calculated all normalized read counts, p-values, and fdr values listed in []. all raw and processed files from the rna […]


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NGSUtils in publications

 (12)
PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] based on the number of mismatches (mapping only perfect matches, then 1-mismatch, then 2, …), one can perform an intensive mapping of all possibilities at once, and use downstream tools like ngsutils [] to parse their desired level of matching preciseness from the output file. a second approach is to randomly divide the multi-mapping reads to their best positions in the genome (for […]

PMCID: 5957051
PMID: 29780667
DOI: 10.7717/peerj.4686

[…] to the hg19 human genome. we retained uniquely aligned reads with a minimum splice junction overhang of five nucleotides using default parameters. the gene expression level was estimated using the ngsutils tool (version 0.5.9) () with default parameters for calling gene expression. the splicing level (psi) was estimated using a probabilistic model called mixture of isoforms (miso) (). […]

PMCID: 5535924
PMID: 28677627
DOI: 10.3390/ijms18071433

[…] and butterfly for de novo transcriptome assembly. quantification of the assembly was performed with kallisto., quality parameters and general statistics were obtained by fastqc, the fastqutils from ngsutils [] and from the rna-seq provider’s report. the transcripts were then functionally annotated using blastx and uniprot/swissprot (version 11_2016). as databases. the e-value cutoff for blastx […]

PMCID: 5486022
PMID: 28587253
DOI: 10.3390/ijms18061199

[…] and construct possible splice forms. quantification of the assembly was performed with kallisto []., quality parameters and general statistics were obtained by fastqc [], the fastqutils from ngsutils [] and from the rna-seq provider’s report., annotation of the trinity assembled transcripts: blastx (e-value cutoff 10e -3) was applied to align the transcripts to uniprot/swissprot (version […]

PMCID: 5126689
PMID: 27897201
DOI: 10.1038/srep37821

[…] clipping algorithm. rna-seq reads were then mapped by bowtie v1.0.0, to gencode lncrna reference (release 17) for lncrna (including lincrna) annotations. transcript abundances were quantified using ngsutils. 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 were further identified […]


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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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