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NextGENe specifications

Information


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

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  • person_outline NextGENe Team <>

NextGENe in pipelines

 (15)
2018
PMCID: 5821328
PMID: 29466388
DOI: 10.1371/journal.pone.0192377

[…] 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 […]

2018
PMCID: 5839370
PMID: 29515789
DOI: 10.18632/oncotarget.24273

[…] 2 × 150 paired-end sequencing strategy., primary basecall sequencing outputs were converted to fastq format and demultiplexed on illumina’s basespace. read trimming and alignment were performed with nextgene software (softgenetics, state college, pa). reads with median base phred33 quality score ≥ 10, ≤ 3 uncalled bases, ≥ 20 total bases called, and with ≤ 3 bases of quality ≤ 10 were retained […]

2018
PMCID: 5915132
PMID: 29707124
DOI: 10.18632/oncotarget.24770

[…] san diego, usa). the analyses were performed on the illumina misequ® and the nextseq system (illumina, ca, usa). after sequencing, mutations in brca1, brca2 and tp53 were identified with the help of nextgene and geneticist assistant softwares. pathogenicity for new mutations that were not found in the database was determined and categorized using prediction tools like sift, aligngvgd, mutation […]

2017
PMCID: 5440144
PMID: 28514307
DOI: 10.1097/MD.0000000000006914

[…] 2.2.58 software (illumina, inc., san diego, ca) with the new versions of hiseq control software and real time analysis. the reads were mapped to the reference human genome (human 37.3; snp135) using nextgene software (softgenetics llc, state college, pa). wes generated a total of 34,350 variants. the ingenuity variant analysis (ingenuity systems, mountain view, ca) was used to analyze […]

2017
PMCID: 5532258
PMID: 28751748
DOI: 10.1038/s41598-017-06912-7

[…] using the ion ampliseq™ cancer hotspot panel v2 (thermo fisher scientific). raw sequence data were trimmed, classified with xenome software to eliminate as many mouse reads as possible, aligned in nextgene and checked for variants using nextgene v 2.3.4.4 and v2.4.1 software (softgenetics)., fluorescence in situ hybridization analysis was performed in 24 μ-thick paraffin sections by counting […]


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NextGENe in publications

 (141)
PMCID: 5955881
PMID: 29769598
DOI: 10.1038/s41598-018-26040-0

[…] processing of raw sequencing data was performed to analyze spectrum of genetic variants, such as single nucleotide variants and short insertions or deletions, and copy number variations (cnvs) using nextgene software (softgenetics, state college, pa) according to standardized biostatistical methods for ngs data (detailed setting in supplementary methods). nonsynonymous variants in exons […]

PMCID: 5932755
PMID: 29720203
DOI: 10.1186/s13023-018-0812-8

[…] was performed on a miseq desktop sequencer from illumina (illumina, california, usa) with 2 × 150 bp sequencing kit (20 samples per run)., data were analysed by two independent software tools - nextgene (nextgene 2.41, softgenetics, pennsylvania, usa) and surecall (surecall 3.0.3.x, agilent, california, usa)., nextgene analysis was performed with default settings., surecall analysis […]

PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355

[…] 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 […]

PMCID: 5906716
PMID: 29707521
DOI: 10.3389/fonc.2018.00109

[…] amplification of libraries, loading on 316 chip v2, was performed with the ion chief system®, while sequencing was executed using the ion pgm® machine (life technologies). ion reporter® and nextgene® v.2.3.4 (softgenetics, usa) software were used to perform bioinformatics analysis, including optimized signal processing, base calling, sequence alignment (hg19 reference), and variant […]

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

[…] 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., all variants were first […]


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