TJGR things just got real Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012) Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030 Other Resources: OysterDB (Blast, Downloads) | Related manuscript: doi:10.1038/nature11413 .......................................................................................................................

[ http://genefish.wikispaces.com/page/xml/crassostreome?v=rss_2_0]

oyster.v9_M

Sequence	FASTA	60 Sequences; 75 MB
BSMAP	SAM	BS MBD
RNAseq	SAM	PROPS: DH
RNAseq	SAM	PROPS: BBC
RefMap	SAM	MBD Library
Annotation	BED	BS MBD CG features (no scores)
Annotation	BED	BS MBD CG features (with scores)
Annotation	BED	BS MBD CG features (0-20%)
Annotation	BED	BS MBD CG features (20-70%)
Annotation	BED	BS MBD CG features (70-100%)
Annotation	GFF	Tandem Repeats [Phobos] (imperfect search)
Annotation	BED	Tandem Repeats (interval and ID only)
Annotation	BED	Complement to CDS features
Annotation	GFF	CG motifs
Annotation	GFF	CG motifs non overlap w BS MBD CG (~250k)
Annotation	GFF	CG motifs with methylation status (~500k)
Annotation	BED	CG motifs(~500k) (interval and ID only)
Annotation	BED	50bp region (up and down) flanking CG motifs(~500k)
Sequence	FASTA	50bp region (up and down) flanking CG motifs(~500k)
Annotation	GFF	CG motifs (of 500k) that overlap with Tandem Repeats
Annotation	Blast Table	Transposable Elements: RepBase inv Blast
Annotation	BED	Transposable Elements: evalue 1E-10
Annotation	BED	Transposable Elements: evalue 1E-10; single directionality
Data	Tab Text	Interval Join: CG motifs(~500k) and TEs (RepBase)
Data	Tab Text	Interval Join: CG motifs(~500k) and Repeats (Phobos)
Data	Tab Text	Interval Join: CG motifs(~500k) and exons (CDS)
Data	Tab Text	Interval Join: CG motifs(~500k) and closest non overlapping exons
Data	Tab Text	Interval Join: CG motifs(~500k) not overlapping w/ mRNA (extragenic)

Description: Genomic scaffolds longer that 1M bps


oyster.v9_90

Sequence	FASTA	1670 Sequences; 488 MB
Annotation	Tab Text	Tiling Array Design v1

Description: Longest genomic scaffolds (1670; 14%) that cover over 90% of genome.


oyster.v9_proteome

Sequence	FASTA	[.gz] 28027 protein sequences (via gigadb.org)
Sequence	FASTA	28027 protein sequences (local)
Annotation	Blast Table	Blastp Swiss-Prot evalue: 10
Annotation	Blast Table	Blastp Swiss-Prot evalue: 1E-05
Annotation	Blast Table	Blastp Estrogen Biosynthetic Process; 1E-20, 4 max_targets, (details)

Description: Proteins

oyster.v9_genes

Sequence	FASTA	[.gz] 28027 gene (CDS only) sequences (via gigadb.org)
Sequence	FASTA	28027 gene (CDS only) sequences (local)
Annotation	Blast table	Blastx Swiss-Prot evalue: 1E-05
Data	Tab Text	Number of exons per gene
Annotation	Tab Text	Corresponding SPID and evalues
Annotation	Tab Text	Corresponding SPID, evalues, and descriptions
Annotation	Tab Text	Corresponding SPID, evalues, and GO# (using recent GO file)
Annotation	Tab Text	Corresponding SPID, evalues, and GO and GOslim

Description: Coding sequence



oyster.v9

Sequence	FASTA	[.gz] 11969 Sequences (via gigadb.org)
Sequence	FASTA	[.gz] 11969 Sequences (local)
Sequence	FASTA	11969 Sequences (local) 560MB
Annotation	GFF	[.gz] gene features (via gigadb.org)
Annotation	GFF	gene features (CDS and mRNA)
Annotation	GFF	gene features (CDS only)
Annotation	BED	gene features (CDS only) (interval and ID)
Annotation	GFF	gene features (mRNA only)
Annotation	BED	gene features (mRNA only)
Annotation	GFF	promoter region (1000bp 5' of mRNA)
Annotation	GFF	mRNA GOslim = cell adhesion or signal transduction or cell-cell signaling
Annotation	GFF	mRNA GOslim = DNA metabolism or RNA metabolism or protein metabolism
Annotation	GFF	DESeq (p<0.05) Gill v Male Gonad RNA-seq from Zhang et al

Description: Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012) Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030

TGAGA (alpha) towards getting a gigas assembly (alpha) ................................................................................................................................................

cgigas_alpha_v0.4.0

Sequence

FASTA

230,270 Sequences

Description: Independent assembly of 19 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.
Combination of assemblies v0.2.0 and v0.3.1.

cgigas_alpha_v0.3.2

Sequence	FASTA	272 Sequences
Annotation	GFF v1 (gff)	blastn Sigenae8
Annotation	BED v1 (bed)	blastn Sigenae8
Visual	Blast Directionality (htm)	based on BED v1
Annotation	GFF v2 (gff)	blastn Sigenae8 (includes gene description)
Annotation	GFF v3 (gff)	blastn Sigenae8 GOslim= cell adhesion or signal transduction or cell-cell signaling
Annotation	GFF v3 (bed)	blastn Sigenae8 GOslim= cell adhesion or signal transduction or cell-cell signaling
Annotation	GFF v4 (gff)	blastn Sigenae8 GOslim= DNA metabolism or RNA metabolism or protein metabolism
Annotation	GFF v4 (bed)	blastn Sigenae8 GOslim= DNA metabolism or RNA metabolism or protein metabolism
Annotation	MicroSatellite (GFF3)	MicroSatellite Regions (HP)
Annotation	Repeat_Regions(GFF3)	Regions that are repeated 10 or more times(HP)
Annotation	Repeat_Regions v1 (GFF3)	Regions that are repeated 10 or more times, derivative regions omitted (HP)
Annotation	Repeat_Regions v2 (GFF3)	Fixed orientation and score issues (HP)
Annotation	Repeat_Regions v3 (GFF3)	Identified some Retrotransposon regions from Repbase (HP)
Annotation	Repeat_Regions(BED)	Regions that are repeated 10 or more times(HP)
Annotation	Repeat_Regions v1 (BED)	Regions that are repeated 10 or more times, derivative regions omitted(HP)
Annotation	GFF v5 (gff)	Tandem repeats (Geneious:Phobos)
Annotation	GFF v6 (gff)	Transcription Factors (Geneious)
Alignment	RefMap MBD_meth (bed)	gill tissue
Alignment	RefMap MBD_unmeth (bed)	gill tissue
Alignment	RNAseq BB3 (bed)	gill tissue
Alignment	RNAseq DH3 (bed)	gill tissue
Alignment	RefMap larvae_SRP002286 (bed)	larvae
Alignment	RefMap larvae_SRP004696 (bed)	Two 454 SRA files - larvae
Motif	CG motifs (gff)
BSMAP	BSMAP_MBD_all (gff)	Bisulfite-seq 10x cov ; all
BSMAP	BSMAP_MBD_0 (gff)	Bisulfite-seq 10x cov ; 0% methylated
BSMAP	BSMAP_MBD_1_9 (gff)	Bisulfite-seq 10x cov ; 1-9% methylated
BSMAP	BSMAP_MBD_10_49 (gff)	Bisulfite-seq 10x cov ; 10-49% methylated
BSMAP	BSMAP_MBD_50_89 (gff)	Bisulfite-seq 10x cov ; 50-89% methylated
BSMAP	BSMAP_MBD_90_100 (gff)	Bisulfite-seq 10x cov ; 90-100% methylated
Visual	Track Visualization BS (Galaxy)	Tracks include: exon annotation, RNA-seq, select GO terms, CpG methylation
Visual	Track Visualization 454 (Galaxy)	Tracks include: RefMap larvae_SRP004696 (bed)
Annotation	bigwig 1
Annotation	bigwig 2

Description: Independent assembly of 10 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset. Sequences greater than 20k bp retained. Cgigas BAC clones from NCBI (60) reduced to 53 clusters. Plus 12 select sequences with known genomic structure.



cgigas_alpha_v0.3.1

Sequence

FASTA

500MB

203,216 Sequences

Description: Independent assembly of 10 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.


cgigas_alpha_v0.3.0

Sequence	FASTA	12.3MB	272 Sequences
Annotation	GFF v1 (gff)		blastn Sigenae8
Annotation	BED v1 (bed)		blastn Sigenae8
Alignment	MBD-meth reads (sam)
Alignment	MBD-ummeth reads (sam)
Alignment	RNAseq BB3 (sam)
Alignment	RNAseq DH3 (sam)

Description: Independent assembly of 10 fosmids. Consensus sequences >20,000bp along with publicly available BAC sequences were analyzed using CD-HIT EST to obtain non-redundant dataset. Plus 12 select sequences with known genomic structure.


cgigas_alpha_v0.2.0

Sequence	FASTA	615MB	205,903 Sequences
Annotation

Description: Independent assembly of nine fosmids. Consensus sequences were analyzed using CD-HIT EST to obtain non-redundant dataset.


cgigas_alpha_v0.1.3

Sequence	FASTA	6MB	262 Sequences
Annotation

Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Remaining sequences greater than 20,000 bp are included. Plus 12 select sequences with known genomic structure.


cgigas_alpha_v0.1.2

Sequence	FASTA	215MB	28,538 Sequences
Annotation	BLASTn Sigenae v8 (tsv)	800MB	*rev
Annotation	GFF v1 (gff)	9MB

Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Plus 12 select sequences with known genomic structure.


cgigas_alpha_v0.1.1

Sequence	FASTA	215MB	28,526 Sequences
Annotation

Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset.


cgigas_alpha_v0.1.0

Sequence	FASTA	5.8MB	250 Sequences
Annotation	BLASTn Sigenae v8 (csv)		top hit
Annotation	SW Sigenae v8 (tsv)		top hit
Annotation	GFF v0 (gff)		12,582 total hits
Annotation	GFF v1 (gff)		3891 hits, gene names
Annotation	GFF v2 (gff)		1105 hits, used rev blast

Description: Independent assembly of nine fosmids. Consensus sequences with greater than 20x average coverage and longer than 5000 bp were analyzed using CD-HIT EST to obtain non-redundant dataset. Remaining sequences greater than 20,000 bp are included.


cgigas_PREalpha_v0.2.0

Sequence	FASTA		12 sequences
Annotation	GFF v1 (gff)
Annotation	GFF v2 (gff)		Exons only
Alignment	MBD-BS reads (sam)

*BLAST option: blastn, megablast select database from menu

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Related Resources

various other genomic resources for the oyster.

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GigasBase

Public Sigenae Contig Browser: Oyster

The Oyster EST contig browser aims to produce and maintain an automatic annotation of Oyster EST libraries. This database GigasDatabase was initiated within the frame of the AquaFirst European project, it now gathers EST sequences produced by a Marine Genomics Europe project (GOCE-CT-2004-505403) and a Genoscope project. GigasDatabase is regularly updated in the context of the ANR project "Gametogenes" (ANR-08-GENM-041).

GigasDatabase Assemblies

Version 8
cgigas_all_contigs_v8.fa
cgigas_all_contigs_v8_BESTHIT.tsv
cgigas_all_contigs_v8_ontology.tsv

Archived GigasDatabase Assemblies

Version 6
Sigenae_v6_assembly.fa
Sigenae _v6_SPhits.xls

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NCBI

Crassostrea gigas Entrez Records
Crassostrea virginica Entrez Records

NCBI: SRA

Crassostrea gigas
FASTA export of quality trimmed reads (export date 02/10/11)

Misc

Cgigas_BAConly.fa (export date 01/31/11)
Cgigas_genomic_NCBI.fa (export date 01/31/11)

Roberts Lab Submissions

Crassostrea Nucleotide Database entries
Crassostrea gigas EST Database entries

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