Supporting data for

Transcript-and annotation-guided genome assembly of the European starling
Stuart KC†, Edwards RJ†, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL, Rollins LA 2021. Transcript- and annotation-guided genome assembly of the European starling

This entry contains the supporting supplementary files, some generated data files, and the code used for transcriptome and genome assembly and annotation. Code will be messy at times, as this was the first genomics project/manuscript I worked on, and I had no idea what I was doing at times. This feeling persists some days. 
If you need help or clarification, feel free to reach out to me. 

And if you are embarking on your own genome assembly, I wish you luck.

SUPPLEMENTARY FILES:
Sv3.10_Supplementary_File_1_starling10xV3.N3L20ID0U.full.html
Sv3.10_Supplementary_File_2_starling10xV5.N3L20ID0U.full.html	
These two files represent the raw program outputs of BUSCOMP, and are used for both discussion of BUSCOMP benchmarking, and also to showcase program capabilities.

DATA:
Sturnus_vulgaris_vAU_1.0.fasta: genome assembly fasta file for S. vulgaris vAU1.0 (S. vulgaris vAU1.1 is uploaded on NCBI, GCA_023376015.1)
Svulgaris.all.gff: associated annotation file for S. vulgaris vAU1.0 (MAKER2 and GEMOMA merged annotation, i.e. final annotation)
vAU_allRepeats.lib.fasta: Custom repeat library generated for S. vulgaris vAU1.0 using the advanced repeat library construction in MAKER2 
vNA_allRepeats.lib.fasta: Custom repeat library generated for S. vulgaris vNA using the advanced repeat library construction in MAKER2
For more information on custom repeat generation, please refer to the manuscript, or visit the MAKER2 website (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced)

CODE:
Code files are PDF of LabArchive notes. Code files have been labelled with to indicate which workflow process and step they refer to (transcriptome/genome/annotation).