Transcript and genome assemblies of Atlantic cod

• Main Authors: Tørresen, Ole K., Nederbragt, Lex
• Format: Dataset
• Language: unknown
• Published: figshare 2016
• Subjects: 60102 Bioinformatics; FOS Computer and information sciences; atlantic cod
• Online Access: https://dx.doi.org/10.6084/m9.figshare.3408247; https://figshare.com/articles/dataset/Transcript_and_genome_assemblies_of_Atlantic_cod/3408247

Described here: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3448-xNEWB454: An assembly based on 454 sequencing reads and sequenced BAC-ends. Assembled with Newbler 3.0. CA454ILM: An assembly based on Illumina and 454 sequencing reads. Assembled with Celera Assembler. CA454PB: An assembly based on Illumina, 454 and PacBio sequencing reads. Assembled with Celera Assembler. ALPILM: An assembly based on Illumina reads. Assembled with ALLPATHS-LG. gadMor2: An assembly reconciliation of NEWB454, ALPILM, CA454PB, CA454ILM put into linkage groups. trinity_cod_rna: A Trinity assembly of Illumina RNA reads from 10.1016/j.redox.2015.06.003. newbler_cod_rna: A Newbler assembly of 454 and Sanger reads from 10.1038/nature10342 and Sanger reads from 10.1186/1471-2164-13-443. isoseq_cod_rna: A IsoSeq clustering of PacBio RNA reads.te_comprehensive_cod_replib: The repeat library used for annotation TEs.repeatmodeler_cod_replib: The repeat library used for annotation. gadMor2_predicted_*_filtered: The predicted proteins/transcripts, filtered at less than 0.5 AED.gadMor2_predicted_transcripts_all: All predicted proteins/transcripts.gadMor2_annotation_filtered_only_gene_models: Only the gene models from the annotation, genes with less than 0.5 AED.gadMor2_annotation_filtered: Only genes with less 0.5 AED, plus everything else (exonerate, blast, repeats etc).gadMor2_annotation_complete: Everything MAKER outputs.