In order to evaluate the quality of our assembly, we compared it to representative genomes of other species of the subfamily *Murinae* available from the NCBI assembly database. The database contained genomes of 13 species, 8 of which were of sufficient quality to have been annotated. We utilized R package *rentrez*, a wrapper for NCBI E-utilities, to retrieve assembly records. These records contained contiguity metrics for the 13 assemblies and BUSCO scores for the 8 assemblies.
This repository contains the following files:
- BUSCO_scores_3in.pdf - a plot of BUSCO % Complete and % Duplicated scores from the 8 annotated *Murinae* assemblies
- Contiguity_stats_3in.pdf - a plot of scaffold N50 and contig N50 values of the 13 *Murinae* assemblies
- Murine_assembly_stats.R - the R script used to retrieve assembly data from NCBI and generate the plots
- Murine_assembly_stats.Rproj - RStudio project file
R session info:
sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.2 [8] ggplot2_3.3.3 tidyverse_1.3.1 rentrez_1.2.3 rvest_1.0.0
loaded via a namespace (and not attached): [1] tinytex_0.31 tidyselect_1.1.1 xfun_0.23 haven_2.4.1 colorspace_2.0-1 vctrs_0.3.8 [7] generics_0.1.0 utf8_1.2.1 XML_3.99-0.6 rlang_0.4.11 pillar_1.6.1 glue_1.4.2 [13] withr_2.4.2 DBI_1.1.1 selectr_0.4-2 dbplyr_2.1.1 modelr_0.1.8 readxl_1.3.1 [19] lifecycle_1.0.0 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 labeling_0.4.2 curl_4.3.1 [25] fansi_0.5.0 broom_0.7.6 Rcpp_1.0.6 backports_1.2.1 scales_1.1.1 jsonlite_1.7.2 [31] farver_2.1.0 fs_1.5.0 digest_0.6.27 hms_1.1.0 stringi_1.6.2 grid_4.1.0 [37] cli_2.5.0 tools_4.1.0 magrittr_2.0.1 crayon_1.4.1 pkgconfig_2.0.3
ellipsis_0.3.2 [43] xml2_1.3.2 reprex_2.0.0 lubridate_1.7.10 assertthat_0.2.1 httr_1.4.2 rstudioapi_0.13 [49] R6_2.5.0 compiler_4.1.0
