Newbler assembly software

Manufactured by Roche

Newbler assembly software is a bioinformatics tool developed by Roche for the assembly and analysis of DNA sequencing data. The software's core function is to assemble fragmented DNA sequences into longer contiguous sequences, known as contigs, to facilitate genome assembly and analysis.

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Lab products found in correlation

Titanium platform, by Roche (1 mentions)

Close spelling variants of this product

Newbler software Newbler

2 protocols using newbler assembly software

Metagenomic Fosmid Library Sequencing

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A total of 3,300 randomly selected fosmid clones were sequenced on one full lane of the 454 GS-FLX Genome Sequencer System using the Titanium platform (Roche, Brandford, CT, USA) following the manufacturer’s protocol. Repeats in raw sequenced reads obtained were removed using RepeatMasker (http://www.repeatmasker.org). The vector and host sequences were filtered by BLASTN, with an E-value cutoff of 1e-3. The filtered reads were assembled using the Newbler assembly software, developed by 454 Life Sciences (version 2.6, Roche). Non-overlapping fragment singletons were clustered using the CD-HIT software [58 (link)] to minimize redundant sequences. The overall process of metagenomic data preparation and analysis is summarized in Additional file 1: Figure S1. The entire sequences of the bagasse fosmid library have been deposited to the NCBI Sequence Read Archive (SRA), which can be accessed using the accession number: SRX493840.

Mhuantong W., Charoensawan V., Kanokratana P., Tangphatsornruang S, & Champreda V. (2015). Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnology for Biofuels, 8, 16.

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De novo genome assembly using Newbler

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Roche’s Newbler assembly software was used to perform de novo genome assemblies, using 454-FLX sequence data. The contigs were ordered by alignment to the reference genome of strain PG21 (Accession: PRJNA41875) using Mauve (Genome Evolution Laboratory, University of Wisconsin-Madison, WI)^{64 (link)}. The genome of AF1 was closed by polymerase chain reaction (PCR) and Sanger sequencing.

Allen-Daniels M.J., Serrano M.G., Pflugner L.P., Fettweis J.M., Prestosa M.A., Koparde V.N., Brooks J.P., Strauss JF I.I.I., Romero R., Chaiworapongsa T., Eschenbach D.A., Buck G.A, & Jefferson K.K. (2015). Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intra-amniotic infection. American journal of obstetrics and gynecology, 212(6), 779.e1-779.e13.

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