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Genomic Resources

Here we try to compile genomic resources such that they are readily available and somewhat described. An effort will be made to keep respective index files alongside so these files can be directly used in IGV etc.

Related Resources - Archived Versions of this page - 091319;


Chionoecetes bairdi

Genomes

Transcriptomes

Assembly Stats Table (Google Sheet)

RNA-seq sample list


Crassostrea gigas - cgigas_uk_roslin_v1

Crassostrea gigas - oyster_v9

Related Resources

Genome:

  • Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa : http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa

    • MD5 = 6de9d1239eb10ea0545bed6c4e746d6c

    • FastA index (samtools faidx) : http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.fai

Bisulfite Genome:

Genome Feature Tracks

  • Cgigas_v9_gene.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff

  • Cgigas_v9_exon.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff

  • Cgigas_v9_intron.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff

  • Cgigas_v9_TE.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff

  • Cgigas_v9_CG.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff

    • index: https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff.idx
  • Cgigas_v9_1k5p_gene_promoter.gff : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff

  • Cgigas_v9_COMP_gene_prom_TE.bed : https://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed

  • Crassostrea_gigas.oyster_v9.40.gff3 : http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.40.gff3

    • MD5 = 90a747fbc94a0a9225c43f75cc40b9db
  • Crassostrea_gigas.oyster_v9.40.abinitio.gff3 : http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.40.abinitio.gff3

    • MD5 = c2a8c388f5a8afb22a115d61dee3dda0
  • Crassostrea_gigas.oyster_v9.40_mRNA.gff3

  • grep "mRNA" Crassostrea_gigas.oyster_v9.40.gff3 > Crassostrea_gigas.oyster_v9.40_mRNA.gff3

Crassostrea virginica

NCBI FTP

Genomes:

  • Cvirginica_v300.fa : http://owl.fish.washington.edu/halfshell/genomic-databank/Cvirginica_v300.fa

    • MD5 = f9135e323583dc77fc726e9df2677a32

    • FastA index (samtools faidx)

  • GCF_002022765.2_C_virginica-3.0_genomic.fna : ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/022/765/GCF_002022765.2_C_virginica-3.0/GCF_002022765.2_C_virginica-3.0_genomic.fna.gz

    • compressed version of Cvirginica_v300.fa (same files)

Bisulfite Genomes:

  • Cvirginica_v300_bisulfite.tar.gz : http://owl.fish.washington.edu/halfshell/genomic-databank/Cvirginica_v300_bisulfite.tar.gz

    • Gzipped tarball of bisulfite genome for use with Bismark

    • Creation details here

Genome Feature Tracks

  • C_virginica-3.0_Gnomon_mRNA.gff3 : http://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_mRNA.gff3

  • C_virginica-3.0_Gnomon_exon.bed : http://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_Gnomon_exon.bed

  • C_virginica-3.0_intron.bed : http://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_intron.bed

  • C_virginica-3.0_CG-motif.bed : http://eagle.fish.washington.edu/Cvirg_tracks/C_virginica-3.0_CG-motif.bed

    • MD5 = f88c171bccf45a6f3afcf455b6be810f

    • Dead link in this Jupyter Notebook obscures details on how this was generated (via Galaxy):

      • https://github.com/sr320/nb-2018/blob/master/C_virginica/22-CG-track.ipynb
  • C_virginica-3.0_TE-all.gff : http://owl.fish.washington.edu/halfshell/genomic-databank/C_virginica-3.0_TE-all.gff

    • MD5 = d0d81fc6cf7525bc2c61984bee23521b

    • Details

  • C_virginica-3.0_TE-Cg.gff : http://owl.fish.washington.edu/halfshell/genomic-databank/C_virginica-3.0_TE-Cg.gff

    • MD5 = 83cd753c171076464fee1165b7e1c6ba

    • Details


Hematodinium sp. (Host: Chionoecetes bairdi)

Transcriptomes

Assembly Stats Table (Google Sheet)


Metacarcinus magister (Cancer magister)

Genome:

  • mmag_pilon_scaffolds.fasta

    • MD5 = 5dfa2ba11edf0ff8191f112e0b1378d1

    • Not shared publicly until permission received from NOAA.

    • Roberts Lab members can access on Owl: /web/halfshell/genomic-databank/mmag_pilon_scaffolds.fasta

    • Original filename: pilon_scaffolds.fasta

    • FastA index (samtools faidx)

      • mmag_pilon_scaffolds.fasta.fai

Ostrea lurida

Genome:

  • Olurida_v081.fa : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa

    • MD5 = 3ac56372bd62038f264d27eef0883bd3

    • This is v080 with only contigs > 1000bp. Details of how v080 was reduced found here.

    • FastA index (samtools faidx)

      • Olurida_v081.fa.fai : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa.fai
  • Olurida_v080.fa : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v080.fa

    • MD5 = 9258398f554493e08fdc30e9c1409864

    • FastA index (samtools faidx)

      • Olurida_v080.fa.fai : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v080.fa.fai
    • Also known as pbjelly_sjw_01. Details found here, though confirmation would be good.

Bisulfite Genomes:

  • Olurida_v080_bisulfite.tar.gz : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v080_bisulfite.tar.gz

  • Gzipped tarball of bisulfite genome for use with Bismark

  • Creation details here

Transcriptomes:

Tissue-specific transcriptomes generated by Katherine Silliman

Genome Feature Tracks


Panopea generosa

Genome:

Bisulfite Genome:

Genome Feature Tracks:


Transcriptome:

  • Pgenerosa_transcriptome_v5.fasta : http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_transcriptome_v5.fasta

    • MD5 = 5a21424ecbc88c3b01daefe56bed79da

Transcriptome generated from various libaries - details here


QPX

Genome:

  • QPX_v017.fasta : http://eagle.fish.washington.edu/QPX_genome/QPX_v017.fasta

CLC v5.1 Mismatch cost = 2; Perform scaffolding = Yes; Mapping mode = Map reads back to contigs (slow); Deletion cost = 3; Similarity fraction = 0.9; Length fraction = 0.8; Insertion cost = 3; Update contigs = Yes; Automatic word size = Yes; Minimum contig length = 10000; Automatic bubble size = Yes; input: filtered_QPX_DNA_GTGAAA_L001_R1 trimmed.

CLC v5.1 Mismatch cost = 2; Perform scaffolding = Yes; Mapping mode = Map reads back to contigs (slow); Deletion cost = 3; Similarity fraction = 0.9; Length fraction = 0.8; Insertion cost = 3; Update contigs = Yes; Automatic word size = Yes; Minimum contig length = 10000; Automatic bubble size = Yes; input: filtered_QPX_DNA_GTGAAA_L001_R1 trimmed.

De novo assembly was performed with Genomics Workbench v. 5.0 (CLC Bio, Germany) on quality trimmed sequences with the following parameters: mismatch cost = 2, deletion cost = 3, similarity fraction = 0.9, insertion cost = 3, length fraction = 0.8 and minimum contig size of 100 bp for genomic data and 200 bp for transcriptomic data. In order to remove ribosomal RNA sequences from the transcriptome data, consensus sequences were compared to the NCBI nt database using the BLASTn algorithm [59]. Sequences with significant matches (9) were removed and not considered in subsequent analyses.

Manuscript: https://doi.org/10.1371/journal.pone.0074196

Transcriptome:

QPX_Transcriptome v2.1

Subset of version 1 (v1) that only includes sequences with e-value < 1E-20. Based on Swiss-Prot blastx output, all sequences are oriented 5' - 3'. nucleotides between stop codons; minimum size 200.