Gs reference mapper software

Manufactured by Roche

The GS Reference Mapper software is a bioinformatics tool designed for aligning and analyzing genomic sequences. It provides a comprehensive solution for mapping sequencing data to reference genomes, facilitating the identification and analysis of genomic variations.

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Lab products found in correlation

Gs flx titanium series, by Roche (3 mentions) Methylcap kit, by Diagenode (1 mentions) Qiaquick pcr purification kit, by Qiagen (1 mentions) Gs flx titanium rapid library preparation kit, by Roche (1 mentions) 454 gs junior platform, by Roche (1 mentions) Abi prism 3100, by Thermo Fisher Scientific (1 mentions) Dna shearing system, by Covaris (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions) Gs de novo assembler software, by Roche (1 mentions) Gs junior, by Illumina (1 mentions) Oligotex mrna mini kit, by Qiagen (1 mentions) Clc genomics workbench v6, by Qiagen (1 mentions) Oligotex mrna kit, by Qiagen (1 mentions) Rneasy kit, by Qiagen (1 mentions)

Close spelling variants of this product

GS Reference Mapper (14 citations)

6 protocols using gs reference mapper software

Methyl-Seq of Human Promoters

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First, DNA was fragmented by nebulization during 1min30sec at 2.1 bar of nitrogen pressure. After DNA purification using Qiaquick PCR purification kit (Qiagen), methylated DNA was captured using MethylCap kit (Diagenode) following the supplier recommendations. Libraries were generated using GS FLX Titanium Rapid Library Preparation Kit (Roche). Finally, emPCR amplification and 454 sequencing were performed according to the manufacturer's protocol (emPCR Amplification Manual- Lib-L LV and Sequencing Method Manual-GS FLX Titanium Series, Roche). Methyl-Seq data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-5468.
Sequence reads were aligned on the human genome (hg19) with GS Reference Mapper software (Roche) and mapped on the human proximal promotors using a home-made software named AGSA. Data was then normalized by calculating the 'reads per million mapped reads' (RPM) for each gene. When the RPM value was below the threshold of 0.3, then it was considered as background noise and replaced by zero.

Privat M., Rudewicz J., Sonnier N., Tamisier C., Ponelle-Chachuat F, & Bignon Y.J. (2018). Antioxydation And Cell Migration Genes Are Identified as Potential Therapeutic Targets in Basal-Like and BRCA1 Mutated Breast Cancer Cell Lines. International Journal of Medical Sciences, 15(1), 46-58.

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Genome Resequencing of Evolved Microbes

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The genomes of the ancestor R0 and the evolved cell population R7 were resequenced using a next-generation sequencer (Junior, Roche). Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions. Whole-genome shotgun sequencing by the 454 GS Junior platform (Roche) was performed according to the manufacturer’s instructions. The sequence reads were assembled using Newbler 2.7 and aligned using the GS Reference Mapper software (ver. 2.6; Roche). Approximately 99% of the reads in each dataset (DRA003743, DDBJ) were uniquely mapped to the MDS42 genome (AP012306, DDBJ). The mutations were analyzed using the GS Reference Mapper software. The candidate mutations were further determined by Sanger methods of the genome samples subjected to a resequencing analysis using a genetic analyzer (ABI PRISM 3100, Applied Biosystems). Sequencing was performed to both the purified genomes and the cell pellets of these populations. In addition, the cell populations (R0–R7) acquired in the experiments of growth curves were repeatedly sequenced for further verification.

Ying B.W., Honda T., Tsuru S., Seno S., Matsuda H., Kazuta Y, & Yomo T. (2015). Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLoS ONE, 10(8), e0135639.

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Vibrio cholerae Genome Assembly and Annotation

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The raw sequencing reads, from both the Roche GS Junior (SFF file) and Illumina MiSeq (FASTA file), were assembled into contigs using GS de novo Assembler software (version 2.7; Roche). Assembled contigs were analyzed using NCBI BLAST to confirm V. cholerae species identification. Annotation of assembled contigs was done using the RAST Annotation Server (8 (link)) and the annotation service of the Institute for Genome Sciences (Baltimore, MD). All completed genome projects for Vibrio cholerae in the NCBI database were utilized as reference strains for mapping of reads from the Philippines strains, using GS Reference Mapper software (version 2.7; Roche).

Klinzing D.C., Choi S.Y., Hasan N.A., Matias R.R., Tayag E., Geronimo J., Skowronski E., Rashed S.M., Kawashima K., Rosenzweig C.N., Gibbons H.S., Torres B.C., Liles V., Alfon A.C., Juan M.L., Natividad F.F., Cebula T.A, & Colwell R.R. (2015). Hybrid Vibrio cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines. mBio, 6(2), e00047-15.

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Transcriptome Analysis by 454 Sequencing

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First, mRNA were purified using Oligotex mRNA mini kit (Qiagen). cDNA libraries were then generated following the GS-FLX Titanium cDNA Rapid Library Preparation Method Manual (Roche). Finally, emPCR amplification and 454 sequencing were performed according to the manufacturer's protocol (emPCR Amplification Manual- Lib-L LV and Sequencing Method Manual-GS FLX Titanium Series, Roche). RNA-Seq data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-5465.
Sequence reads were aligned on the human genome (hg19) with GS Reference Mapper software (Roche) and mapped on the human exome using a home-made software named AGSA. Data was then normalized by calculating the 'reads per kilo base per million mapped reads' (RPKM) for each gene. When the RPKM value was below the threshold of 0.3, then it was considered as background noise and replaced by zero.

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Sequence Mapping Comparison: CLC vs GS Workbench

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Sequence data mapping was performed using CLC Genomics Workbench v6.0.4 (CLC Inc, Aarhus, Denmark). CLC Reference Mapper was run with default settings (Insertion cost = 3, Deletion cost = 3, Mismatch cost = 2, Length fraction = 0.5 and similarity fraction = 0.8). CLC default settings were arbitrarily assigned as low stringency settings. Medium stringency settings were arbitrarily defined as Insertion cost = 3, Deletion cost = 3, Mismatch cost = 2, Length fraction = 0.7 and similarity fraction = 0.8. High stringency settings were defined as Insertion cost = 3, Deletion cost = 3, Mismatch cost = 3, Length fraction = 1.0 and similarity fraction = 1.0. GS Reference Mapper software (v2.0.01.14; Roche/454) was used to produce reference-guided assemblies of each of the Roche datasets with respect to the DENV-1 genome (GenBank; DVU88536).

Frey K.G., Herrera-Galeano J.E., Redden C.L., Luu T.V., Servetas S.L., Mateczun A.J., Mokashi V.P, & Bishop-Lilly K.A. (2014). Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood. BMC Genomics, 15, 96.

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Transcriptome Profiling by RNA-Seq

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Total cellular RNA was extracted from cell lines using RNeasy kit (Qiagen), and mRNA was purified using Oligotex mRNA kit (Qiagen). cDNA librairies were then generated following the GS-FLX Titanium cDNA Rapid Library Preparation Method Manual (Roche). Finally, emPCR amplification and 454 sequencing were performed according to the manufacturer's protocol (emPCR Amplification Manual- Lib-L LV and Sequencing Method Manual-GS FLX Titanium Series, Roche). Sequence reads were aligned on the human genome (hg19) with GS Reference Mapper software (Roche) and mapped on the human exome using an home-made software named AGSA (15). Data was then normalized by calculating the 'reads per kilo base per million mapped reads' (RPKM) for each gene. When the RPKM value was below the threshold of 0.3, then it was considered as background noise and replaced by zero. mRNA-Seq data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-5465.

Privat M., Cavard A., Zekri Y., Ponelle-Chachuat F., Molnar I., Sonnier N, & Bignon Y.J. (2020). A high expression ratio of RhoA/RhoB is associated with the migratory and invasive properties of basal-like Breast Tumors. International Journal of Medical Sciences, 17(17), 2799-2808.

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