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NextGENe specifications


Unique identifier OMICS_01131
Name NextGENe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline NextGENe Team

NextGENe citations


Germline mutation in the TP53 gene in uveal melanoma

Sci Rep
PMCID: 5955881
PMID: 29769598
DOI: 10.1038/s41598-018-26040-0

[…] NextGENe® Software was used for the analysis of the sequencing data, and CNV analysis. The Pindel tool was used to detect break points of large deletions and medium sized insertions. The R package SNP […]


Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early onset/familial prostate cancer

PLoS Genet
PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355
call_split See protocol

[…] For variant analysis, sequences were aligned to the reference genome (GRCh37/hg19) using three different alignment and variant calling software: Isaac Enrichment (v2.1.0), BWA Enrichment (v2.1.0) and NextGENe (v2.4.1; Softgenetics, State College, PA, USA), as previously described []. Briefly, for variant annotation and filtering, .vcf (variant call format) files from the three software were import […]


Phenotypic Progression of Stargardt Disease in a Large Consanguineous Tunisian Family Harboring New ABCA4 Mutations

PMCID: 5875050
PMID: 29736279
DOI: 10.1155/2018/1030184

[…] le preparation kit and Illumina HiSeq2000 at a mean coverage ×31. Sequence reads were aligned to the human genome reference sequence (build hg19), and variants were identified and annotated using the NextGene software package v.2.3.5. (Softgenetics, State College, PA). To determine the regions of homozygosity from the WES data, we used an in-house developed Excel macro. […]


Full Genome Sequence of Infectious Laryngotracheitis Virus (Gallid Alphaherpesvirus 1) Strain VFAR 043, Isolated in Peru

Genome Announc
PMCID: 5843735
PMID: 29519822
DOI: 10.1128/genomeA.00078-18

[…] n of the inoculated CAMs using a phenol-chloroform method ().Whole-genome sequencing was performed by Macrogen, Inc. (South Korea), using a HiSeq 2000 platform. The reads were assembled de novo using NextGene (), with a coverage of 87×. The open reading frames (ORFs) were analyzed and annotated using SnapGene (GSL Biotech LLC) and Artemis (). BLAST () was performed to determine gene identity. The […]


Genetic defects in ciliary genes in autosomal dominant polycystic kidney disease

PMCID: 5838416
PMID: 29527510
DOI: 10.5527/wjn.v7.i2.65

[…] rer’s instructions. The sequencing analyses were performed on the HiSeq 2500 sequencing system (Illumina, United States). Data were analyzed using a software package that was commercially available - NextGENe™ (SoftGenetics, United States). Only variants with a minimum of 50-fold coverage for at least 80% of the targeted bases were included into analysis. Variants were marked as potential errors i […]


Prospecting for viral natural enemies of the fire ant Solenopsis invicta in Argentina

PLoS One
PMCID: 5821328
PMID: 29466388
DOI: 10.1371/journal.pone.0192377
call_split See protocol

[…] eeler Aligner (bwa-0.7.5a), a software package for mapping low-divergent sequences against a large reference genome []. The S. invicta unmapped reads were selected and converted to FASTA format using NextGENe-2.3.4 (SoftGenetics, State College, PA). Each read was then filtered and retained if the median score was ≥ 20 and base number ≥ 25. Unmapped and filtered individual MiSeq sequences were anal […]


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NextGENe institution(s)
SoftGenetics, LLC, PA, USA

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