Sentence examples for using the newbler assembler from inspiring English sources

The reads for the 8 species were assembled using the Newbler assembler and a summary of the sequencing and assembly statistics for the Yersinia genomes is given in Table 2.

The 454 sequence reads were assembled using the newbler assembler with standard settings and using the CLC Genomics Workbench as an alternative assembly method.

Reads were aligned and assembled using the Newbler assembler software provided with the GS FLX instrument.

454 pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche).

Obtained sequencing reads were quality trimmed and assembled using the Newbler assembler software (version 2) by 454 Life Sciences.

Sequences were assembled using the Newbler assembler version 2.3, provided by Roche.

To perform de novo transcriptome assembly with our reads, we used the Newbler assembler (version 2.3) using parameter settings specifically for mRNA assembly (see Supporting Information, Table S5).

Given two sets of 454 reads (readA and readB) from different genomes, we first used the newbler assembler to create two independent sets of contigs, named as contigA and contigB.

The final hybrid assembly of both 454 data and Illuminia data was performed by using the Newbler v.2.6 assembler (default parameters with overlap parameter > = 40 and identity to > =95%, http://www.454.com/products/analysis-software/) [ 69, 70].

All of the H. brasiliensis cDNA data were first filtered by quality scores, presence of adapters, PolyA/T tails and repetitive elements using preprocess.pl Perl script from est2Assembly [ 35], and then assembled into contigs using the Newbler de novo assembler algorithm of the gsassembler (Newbler version 2.7, Roche 454).

A total of 181 contigs were assembled from the ACBU02 "454" genome data using the Newbler and SeqMan Pro assemblers.