Sentence examples for using a reference genome from inspiring English sources

There are several others, including: de novo transcriptome assembly [ 3] and de novo alternative splicing calling [ 4] from transcriptomic NGS data (RNA-seq); metagenome assembly [ 5] from metagenomic NGS data; and genomic variant detection [ 6] from genomic NGS data using a reference genome.

Briefly, contigs were assembled de novo from the short reads and were only oriented using a reference genome by anchoring.

We assembled the E-Pae strain 2250 and I-Pae Illumina datasets de novo (i.e. without using a reference genome) using Velvet 0.7.48 [57].

We had Roche assemble contigs de novo rather than by using a reference genome, developed an algorithm to assemble contigs to pseudomolecules by synteny to the genome of MG1655, and wrote a custom Perl program to find polymorphisms in the aligned genomes.

The processed reads were assembled de novo (i.e., without using a reference genome) with Trinity r20131110 [ 38] (kmer length = 25).

Stacks can identify loci not only de novo as described above but also using a reference genome.

We describe here how the pipeline functions to build a genetic map de novo, and then how it can use a reference genome.

Using a reference pan genome approach (Meric et al. 2014), we investigate core and accessory genome variation, and realized recombination within- and between-species.

CPXV-BR virus was used as a reference genome; all gene positions used are those in CPXV-BR, and only gene families with a member in CPXV-BR were used in the analysis.

Nucleotide sequences of the mitochondrial genes in BA000029.3 need to be updated using the data in this study when used as a reference genome.

The genomes of M. phaseolina and F. oxysporum were compared using MUMmer [ 69] tools to identify regions of synteny, with Aspergillus fumigatus used as a reference genome.