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Newbler specifications

Information


Unique identifier OMICS_01428
Name Newbler
Alternative name GS De novo assembler
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format SFF,FASTA
Output data Consensus sequence (contigs), Corresponding quality scores, Assembly metrics files, Pairwise alignments, Read status file
Output format FASTA,ACE
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for GS De novo assembler

Newbler citations

 (1811)
call_split

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

2018
Sci Rep
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3
call_split See protocol

[…] s obtained after ultracentrifugation were separately sequenced using MiSeq Illumina technology at the Center for Biotechnology (CeBiTec) in Bielefeld, Germany. The reads obtained were assembled using GS de novo Assembler software (gs Assembler, version 2.8, Roche). Plasmid finishing was accomplished using the CONSED software package. Complete closed replicons were automatically annotated by the ge […]

library_books

Complete Genome Sequences of Bacillus Phages Janet and OTooleKemple52

2018
Genome Announc
PMCID: 5946042
PMID: 29748396
DOI: 10.1128/genomeA.00083-18

[…] icroscopy and genome analysis support a Myoviridae morphology for both phages.Phage genomic DNA was sequenced by the Pittsburgh Bacteriophage Institute using Illumina sequencing. The assembly program Newbler was used to produce a single contig from 50,000 reads, resulting in ∼100-fold depth of coverage. Gene annotation was completed using DNA Master (see http://cobamide2.bio.pitt.edu/computer.htm) […]

call_split

Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101

2018
Genome Announc
PMCID: 5946041
PMID: 29748398
DOI: 10.1128/genomeA.00256-18
call_split See protocol

[…] kit. Sequencing was performed by the VIB Nucleomics Core Facility (Leuven, Belgium) using an 8-kb paired-end library and 454 pyrosequencing, as described previously (). Reads were assembled using the GS De Novo Assembler v2.7 with default parameters, followed by gap closure with PCR and Sanger sequencing of the resulting amplicons (VIB Genetic Service Facility, Antwerp, Belgium) based on primers d […]

library_books

Draft Genome Sequence of a “Candidatus Brocadia” Bacterium Enriched from Activated Sludge Collected in a Tropical Climate

2018
Genome Announc
PMCID: 5946052
PMID: 29748410
DOI: 10.1128/genomeA.00406-18

[…] yzed these data using RiboTagger () and observed ∼70% relative abundance for genus “Candidatus Brocadia” (V4 ribotag annotated against SILVA release 119) ().We constructed a metagenome assembly using Newbler v 2.9 (454 Life Sciences) and employed the CONCOCT program to cluster these contigs into 27 putative genome bins (). The most abundant bin contained 168 contigs (length, 1,527 to 114,900 bp; m […]

call_split

Genome Sequence of the Symbiotic Type Strain Mesorhizobium helmanticense CSLC115N Isolated from Lotus corniculatus Nodules

2018
Genome Announc
PMCID: 5946044
PMID: 29748412
DOI: 10.1128/genomeA.00412-18
call_split See protocol

[…] in-house adapted protocol of the NEB prep kit.In total, 7,816,693 sequence reads were obtained, yielding a total of 1,153,487,657 bp of sequence information. The Illumina reads were assembled by the GS de novo assembler software (gsAssembler, version 2.8, Roche) with the final outcome of 145 large contigs (>200 bp). The average contig size was 47,445 bp, with the largest being 379,735 bp. The est […]

library_books

Global evolution and phylogeography of Brucella melitensis strains

2018
BMC Genomics
PMCID: 5946514
PMID: 29747573
DOI: 10.1186/s12864-018-4762-2

[…] ding Q < 15 were delited in Trimmomatic version 0.33 []. Reids with an average quality of Q < 20, as well as reids less than 75 nucleotides long were removed. The genome was assembled in the software Newbler v 3.0 (Roche). Evaluation of the quality of genome assembly was performed using the Quast 3.0 program [], the genomic sequence of B. melitensis 16 M strain (GeneBank: NC003317, NC003318) was u […]

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