Sentence examples for assemblies we used from inspiring English sources

While previous studies used EST assemblies, we used an assembled genome reference and its corresponding gene annotations to determine gene expression resulting in more accurate numbers of expressed genes in a single tissue and the individual contributions of the distinct polyploid genomes.

For the partial assemblies we used the reads generated from each experimental condition.

For each of the Trans-ABySS assemblies, we used k-mer lengths from every odd number starting from 45 to 87.

Given that RNA genes are often present in repeated units which are not resolved in short-read assemblies, we used read coverage values to estimate the copy number of those genes.

In the second round of assemblies, we used more stringent quality filters (length > 250 nucleotides; Q ≥ 29 on 90% of read length), and fixed k-mer length and k-mer coverage to 247 bp and 100, respectively.

As a comparison reference for the aforementioned long-read assemblies, we used the WGS3 assembly, which is the best unfinished Sanger assembly of the D. melanogaster genome (Hoskins et al. 2002).

To align these reads to proposed assemblies, we use Bowtie2 [ 17].

> -wrap-foot> In order to evaluate the effect that different WGA protocols may have in generating a genome assembly, we used the SGA assembler to assemble reads from each of the libraries.

For the chloroplast assembly, we used fully assembled plastomes from H. parviflora var.

To supplement the Velvet-Oases assembly, we used another de novo assembler, Trinity, which was shown to recover more full-length transcripts across a range of sensitivity levels similar to genome alignment methods (Grabherr et al. 2011).

Before whole de novo assembly, we used CAP3 software (ver. 04/15/05) to assemble the 5'- and 3'-end sequences of the same clone in the ESTs.