Sentence examples for pipeline as reference from inspiring English sources

To bypass the limits of single phylogeny or homology methods, in this work we used the Ensembl orthology prediction pipeline as reference [ 27].

3. SNPs are not called in the whole gene filtering method if the corresponding genes have only one SNP expressed, while these SNPs are still used and classified in the mixture model pipeline as long as both the reference and variant allele read counts are above 3 (the predetermined threshold).

This procedure was repeated for each pipeline taking that pipeline as a reference (n), then ordering the probes in ascending order according to the corresponding p value and finally calculating the Spearman correlation with the p values obtained with another pipeline (k).

Trees built by the pipeline also served as references to validate the taxonomic assignments.

Tax4Fun allows easy processing of the output from SILVAngs, QIIME or any other analysis pipeline using the SILVA database as reference.

Using a threshold recommended by Mortazavi et al. [ 210], we filtered low abundance transcripts with FPKM less than 1, and used these as reference sequences for the proteomic pipeline.

We developed a homology-filtering approach used in a high-throughput pipeline in which all known miRNA genes were used as reference miRNAs.

The GATK [16] best practices pipeline for germline SNP and indel discovery in whole-genome and whole-exome sequence (https://software.broadinstitute.org/gatk/best-practices/bp_3step.php case=GermShortWGS) is often used as reference for scalable genomics data analysis pipelines.org/gatk/best-practices/bp_3step.php case=GermShortWGS

We assigned functional annotation to the PERNI data set using the Annocript pipeline [ 38] with default parameters and using the UniprotKB (2014 11 version) as reference.

Sequences were analyzed using phred-phrap-consed software [54] and the pipeline described by Machado et al. [55], using the Genbank sequence NC_000004.11 as reference.

Genome reconstruction and variants identification were performed with the IMR/DENOM ver. 0.3.3 pipeline [ 14] using default parameters and the SL2.40 tomato genome [ 8] as reference.