Additional file 1 of A comprehensive evaluation of long-read de novo transcriptome assembly

Additional file 1: Table S1. Summary of dataset characteristics, parameters and analyses done for each dataset. Table S2. Running time and memory usage for each assembler in each dataset. Table S3. The number of transcripts and genes by SQANTI3 category for each assembly. Table S4. Percentage of repetitive sequences and internally primed sequences. Table S5. Number of transcripts matching BUSCO genes for each assembly usingthe raw uncorrected transcriptome sequences andgenome-corrected transcriptome sequences. Table S6. Correlation coefficient between de novo assembly and reference transcripts and gene abundances. Table S7. Clustering evaluation metrics of native and Corset clustering using SQANTI3 to define true clusters. Table S8. The number of clusters classes as perfect, redundant, mixed and no match for each clustering method. Table S9. Top 10 novel DTEs ranked by FDR in 60 million PCR-cDNA data. Table S10. Top 10 novel DTEs ranked by FDR in dRNA data. Table S11. Novel fusion DTEs in 60 million PCR-cDNA data. Table S12. Novel fusion DTEs in dRNA data. Table S13. Novel DTE with BUSCO hits in pea data.