Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

Supplemental Table 1: All evaluation metrics collected for Johnson et al. 2018 (MMETSP_all_evaluation_matrix.csv)
Supplemental Table 2: Metadata for Supplemental Table 1 (MMETSP_all_evaluation_matrix_METADATA.csv)
Supplemental Notebook 1: comparison between NCBI SRA and iMicrobe sample information (.ipynb, .html)
Supplemental Notebook 2: Trinity version comparisons (.ipyn, .html)
Supplemental Figure 1: Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)
Supplemental Figure 2: Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf)
Supplemental Figure 3: The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)
Supplemental Figure 4: A subset of MMETSP samples. (.pdf and .ipynb)

Other notebooks (all .html) used to generate Figures for Johnson et al 2018:

Johnson_etal_2018_GigaScience_Figures.ipynb
Figures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynb
Figure8_aov.ipynb
MMETSP_transcriptome_assembly_stats.ipynb
make_large_assembly_evaluation_matrix.ipynb

Files located on GitHub:

https://github.com/ljcohen/MMETSP