Dataset for "Nanopore-led long-read genome assembly of the Australian yabby, Cherax destructor"

Intermediate_Assemblies.tar.gz: Intermediate genome assemblies e.g. raw wtdbg assembly (CD.raw.fa), polished wtdbg assembly (CD.cns.fa), 1st pilon polished assembly (CDF2_pilon1.fasta), 2nd pilon polished assembly (CDF2_pilon2.fasta) and RNA-scaffolded assembly (CDF2_pilon2_prna.fasta). Folders with run_"assembly name" are BUSCO output for each of the assembly.

BRAKER2.tar.gz: BRAKER2 genome annotation output containing the initial set of predicted protein-coding genes as well as training intermediate files.

BUSCOv3.tar.gz: BUSCO assessment of publicly available Decapod crustacean genome assemblies

Cdes.filtered.codingseq: Filtered set of protein-coding sequences

Cdes.filtered.faa: Translation of the filtered protein-coding sequences

CDF2.NCBI.fasta.masked.gz: Repeat-masked (softmasked) Cherax destructor genome

Cqua_transcriptome.tar.gz: rnaSPAdes output (combined fasta) of all Cherax quadricarinatus transcriptomes and its reduced dataset generated by EvidentialGene. 

Quast.tar.gz: Quast output of all Decapod crustacean genome assemblies assessed in this study

Repeat_Annotation.tar.gz: Repeat annotation (.gff3) based on Cherax destructor-specific de novo repeat library and its summary (.tbl)

RepeatLibrary.tar.gz: Cherax destructor-specific de novo repeat library generated by RepeatModeler

Wtdbg2_assembly.log: Wtdbg2.5 log file showing exact command used, kmer distribution, memory usage and assembly duration.

CAZY_Annotation.tar.gz: dbCAN2 Identification of CAZy in the selected crustacean proteomes as well as list of cellulase-associated GH groups (glycoside hydrolase). 

Orthofinder.tar.gz: Orthofinder2 output and proteomes of each crustacean used to infer orthologous clustering.

GH9_Analysis.tar.gz: Selected GH9-associated protein sequences, amino acid alignment and IQTree output. 

Cdes_mito.gbf: GenBank file of the annotated complete mitogenome

Cdes.filtered.codingseq: Cherax destructor protein-coding genes with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. 

Cdes.filtered.faa: Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping. 

Cdes.ortholog.list: List of predicted Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping.