Sentence examples for the assembler with from inspiring English sources
The converted data were suitable for chromosomal copy number determination with Magnolya using ABySS (version 1.3.7) as the assembler with a k-mer of 29.
The rank for each metric is given based on relative performance such that the assembler with the best performance has a rank of 1, the second best has a rank of 2 and so on.
It proved to be the assembler with the best performance in generating long contigs, maximizing the percentage of reads assembled, with a higher value than that expected for the optimal assembly (Tables 1 and 2).
Traces were converted into the format required by the Celera Assembler with the tarchive2ca tool, which is part of the A Modular Open Source tool suite http://amos.sourceforge.net/[ 33].
The extension of the seeds is done using the greedy assembler with the set of reads S R - U p ∈ ℑ S R p, where ℑ is the set of all patterns validated during the second step of MixTaR.
The 454 sequence reads were assembled using the newbler assembler with standard settings and using the CLC Genomics Workbench as an alternative assembly method.
The Trinity assembler with the default parameters was used to generate de novo transcriptomes for all species using quality controlled reads [ 3].
For 4 of these 18 we obtained matching reads and quality scores and made a local assembly of the ZF exon using the CAP3 assembler with default settings [ 14], confirming that the exon was present and aligned well with the human ortholog.
All newly generated reads were assembled into contigs using the Newbler assembler with default parameters, generating the following number of contigs larger than 100 bp: G. sphaerica, 24,433; Astrolonche sp., 6426; Phyllostaurus sp., 5056; P. brassicae, 27,333; S. subterranea, 14,531.
All reads were assembled into contigs using the Newbler assembler with default parameters.
Sequence assembly was performed using the Newbler Assembler with sequences masked for oligonucleotide adaptors used in SMART cDNA synthesis and normalization.
