Table 2 Descriptive statistics of the P. longum transcriptomes assembled with transXpress using the Trinity and rnaSPADES assemblers
From: transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
Trinity (v2.13.2) | rnaSPADES (v3.13.0) | |
|---|---|---|
Number of raw sequencing reads (input data) | 16,901,456 (leaf) + 22,900,035 (spike) + 27,496,748 (root) = 67,298,239 total reads | |
Number of assembled transcripts (isoforms) | 268,313 | 296,600 |
Number of reconstructed genes (Trinity estimate) | 132,944 | – |
Min / median / mean / max transcript lengths | 185/577/914/15,159 | 112/363/832/15,665 |
Number of predicted protein ORFs (TransDecoder) | 131,098 | 118,984 |
% of full-length ORFs (TransDecoder estimate) | 54.7 | 60.4 |
Min / median / mean / max ORF lengths | 85/200/282/4982 | 85 / 191 / 255 / 5091 |
Transcriptome completeness (BUSCO, embryophyta_odb10 lineage) | C: 95.2% [S: 10.5%, D: 84.7%], F: 2.7%, M: 2.1% | C: 84.1% [S: 18.6%, D: 65.5%], F: 11.1%, M: 4.8% |
% of reads aligned to the transcriptome (Bowtie2) | 87.5% | 83.3% |