Transcript and genome assemblies of Atlantic cod

posted on 19.10.2016 by Ole K. Tørresen, Lex Nederbragt

Described here: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3448-x

NEWB454: 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.