Sentence examples for using a custom pipeline from inspiring English sources

Genomic breakpoints were detected from mate-pair data using a custom pipeline and the locations of these breakpoints were used as input to readDepth.

Genome annotation was performed using a custom pipeline.

The reads were analyzed from that point on using a custom pipeline written in Python 2.7 and C++.

The fastx_toolkit software package was also used to remove Illumina reads under 50bp, while the 454 and Ion Torrent reads were cleaned using a custom pipeline [ 18].

Functional annotation was performed at the peptide level using a custom pipeline [ 8] that defines protein products and assigns transcript names.

Mutations were found using a custom pipeline written in Python (www.python.org) using the Biopython (biopython.org) and pysam (github.com/pysam-developers/pysam) modules.

We used a custom pipeline to annotate the improved high-quality draft assembly of WH6 as previously described [ 78].

This study used a custom pipeline to identify repeated subsequences from 1 to 250 bases long in 6793306 sequences and 3681160063 nucleotides from 88 genera of vascular plants.

We used a custom pipeline that leveraged remapping protocols using the aligner BWA [ 13] against the closely related reference sequence USA300-FPR3757 as well as de novo assembly with Abyss [ 14] to successfully call polymorphisms ranging from single nucleotide variants (SNV) to large structural rearrangements.

The 454 reads were contigged using a custom perl pipeline and Blat [50] to bin homologous sequences, then cap3 [51] to align sequences in contigs.

Processing and annotation of sequences based on identity to known transcribed RNAs or as novel miRNAs was performed using a custom bioinformatics pipeline described in detail in Supplementary Methods S1.