NGSrich protocols

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NGSrich specifications

Information


Unique identifier OMICS_03603
Name NGSrich
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.7.8
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Peter Frommolt <>

Publication for NGSrich

NGSrich in pipelines

 (2)
2015
PMCID: 4518735
PMID: 25986071
DOI: 10.1136/jmedgenet-2014-102961

[…] using the genome analysis toolkit (http://www.broadinstitute.org/gatk/). by previously described criteria, the low-quality variations were filtered out., target enrichment was analysed using ngsrich. variants were filtered against 1000 genomes data, and all variants with a minor allele frequency (maf) >1% were removed from the analysis. functional annotation of genetic variants […]

2014
PMCID: 4067994
PMID: 24963352
DOI: 10.1186/gm554

[…] including read mapping with burrows-wheeler alignment (bwa) [], duplicate removal with picard, local re-alignment and variant calling with gatk unified genotyper [], enrichment statistics with ngsrich [], and reporting and annotation of variants with custom software []., for copy number analysis, we completed read mapping, duplicate removal, and re-alignment as described above. next […]


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NGSrich in publications

 (5)
PMCID: 5581831
PMID: 28900389
DOI: 10.3389/fncel.2017.00263

[…] genome sequence. (grch37/hg19) using the algorithm bwa-mem (v0.7.15), quality control of input data, alignment, concentration, and coverage of target regions was carried out by fastqc, bamqc, and ngsrich, duplicates was removed by sambamba (v0.6.5). the nucleotide variation was searched with gatk haplotypecaller + unifiedgenotyper (to produce a combined vcf-file)., annotation was performed […]

PMCID: 4796320
PMID: 26969326
DOI: 10.1007/s00439-016-1648-8

[…] with burrows–wheeler alignment (bwa) (li and durbin ), duplicate removal with picard, local re-alignment and variant calling with gatk unified genotyper (mckenna et al. ), enrichment statistics with ngsrich (frommolt et al. ), and variant reporting and annotation with custom-produced software. copy number variant analysis was performed as described (nord et al. ; shearer et al. )., […]

PMCID: 4369643
PMID: 25852744
DOI: 10.3389/fgene.2015.00102

[…] was developed with fastqc v0.10.1 program (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). reads were aligned to the reference genome grch37 with bwa v0.7.5a software (li and durbin, ). ngsrich v0.7.5 software (http://ngsrich.sourceforge.net) used as a control previous to variant detection, and bedtools 2.17.0 (http://bedtools.readthedocs.org/en/latest/#) and picard 1.93 […]

PMCID: 4067994
PMID: 24963352
DOI: 10.1186/gm554

[…] including read mapping with burrows-wheeler alignment (bwa) [], duplicate removal with picard, local re-alignment and variant calling with gatk unified genotyper [], enrichment statistics with ngsrich [], and reporting and annotation of variants with custom software []., for copy number analysis, we completed read mapping, duplicate removal, and re-alignment as described above. next […]

PMCID: 3534602
PMID: 23148716
DOI: 10.1186/1471-2164-13-618

[…] in ≥15% of reads to be considered. variants were compared against our database of deafness variants (deafnessvariationdatabase.org). statistics were calculated using samtools [], bedtools [] and ngsrich []. copy number variants (cnvs) were determined using a previously published method that normalizes sequencing depth among samples, identifies outliers, and calls via a sliding-window method […]


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NGSrich institution(s)
Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Universitat zu Koln, Cologne, Germany; Cologne Center for Genomics (CCG), Universitat zu Koln, Cologne, Germany; Klinik und Poliklinik fur Kinderheilkunde, Abteilung fur Padiatrische Onkologie und Hamatologie, Klinikum der Universitat zu Koln, Cologne, Germany; Zentrum fur Molekulare Medizin Koln (ZMMK), Universitat zu Koln, Cologne, Germany; Neurologische Klinik und Poliklinik, Klinikum Großhadern, Munchen, Germany
NGSrich funding source(s)
Supported by The Koln Fortune Program of the University of Cologne; 115/2010; The German Ministry for Education and Research (BMBF) and The German National Genome Research Network (NGFNplus).

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