Sentence examples for using the trinity package from inspiring English sources

The short reads pooled from the three libraries were primarily assembled into 210,601 contigs using the Trinity package.

De novo assembly of the P. discolor transcriptome was done using the Trinity package [ 63] under default settings.

The reads were also assembled de novo using the Trinity package [ 52] with default settings to serve as additional evidence for gene prediction.

Reads from all life stages were pooled and assembled using the Trinity package [ 17] version r2012-10-05 with the jellyfish k-mer method; RF strand-specific library type; jaccard clip; 200 bp minimum contig length; and paired_fragment_length of 400 bp.

Short reads from seventeen different S. dulcamara cDNA libraries that were sequenced using either Roche GS-FLX or Illumina HiSeq2000 sequencing technologies (Table  1; Additional file 1: Table S1) were combined to build de novo a consensus transcriptome using the Trinity package [ 14].

The resulting 29.5 to 35.7 million high quality reads per library (79 to 80%% of total raw reads) were merged together for de novo transcript assembly using the Trinity package, producing a de novo assembly containing 187,289,921 bases and a total of 196,766 transcripts (Table  2).

Reads combined from all light organ and non-light organ samples were assembled using the Trinity software package [ 50].

De novo assembly of RNA-seq data was carried out using the Trinity software package [ 42] with the maximum length expected between fragment pairs set to 300.

All reads from all libraries were assembled into a genome-free de novo assembly using the Trinity software package (version 2013-02-25) [ 36, 87].

Using the Trinity software package (version r2013-02-15 [ 24] 24]) we assembled all the reads together into a final set of 83,967 unique transcripts (isoforms) after filtering for quality of reads and of assembled transcripts [ 22].

De novo assembly of the clean reads was performed using the Trinity software package, which efficiently constructs and analyses sets of de Bruijn graphs and then fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes [ 62].