Johnson, Lisa Alexander, Harriet Brown, C. Titus 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'<div><br></div><div><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (MMETSP_all_evaluation_matrix.csv)</div><div><b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (MMETSP_all_evaluation_matrix_METADATA.csv)</div><div><b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb, .html)</div><div><b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipyn, .html)</div><div><b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)</div><div><b>Supplemental Figure 2:</b> 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)</div><div><b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)</div><div><b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .ipynb)</div><div><br></div><div>Other notebooks (all .html) used to generate Figures for Johnson et al 2018:</div><div><br></div><div>Johnson_etal_2018_GigaScience_Figures.ipynb</div><div>Figures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynb</div><div>Figure8_aov.ipynb</div><div>MMETSP_transcriptome_assembly_stats.ipynb</div><div>make_large_assembly_evaluation_matrix.ipynb</div><div><br></div><div>Files located on GitHub:</div><div><br></div><div>https://github.com/ljcohen/MMETSP</div> marine;microbial;eukaryotic;transcriptome;sequencing;Bioinformatics;Marine Biology;Microbial Ecology;Microbial Genetics;Ecological Physiology;Marine and Estuarine Ecology (incl. Marine Ichthyology);Gene Expression (incl. Microarray and other genome-wide approaches) 2018-09-14
    https://figshare.com/articles/dataset/Supplemental_Information_for_MMETSP_article_Re-assembly_quality_evaluation_and_annotation_of_678_microbial_eukaryotic_reference_transcriptomes_/7091003
10.6084/m9.figshare.7091003.v4