Genomic Resources

These pages no longer updated, as of 20210126.

Please visit https://robertslab.github.io/resources/ instead.

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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;

• Nightingales (Google Sheet) : Database of all raw high-throughput sequencing data

Species list

C bairdi	C gigas	C virginica	Hematodinium	M magister	O lurida	P generosa	QPX

Chionoecetes bairdi

Genomes

• cbai_genome_v1.01.fasta (18MB)

  • MD5 = 5a08d8b0651484e3ff75fcf032804596

  • BUSCOs: C:0.4%[S:0.3%,D:0.1%],F:0.2%,M:99.4%,n:978

  • FastA index (samtools faidx)

    • cbai_genome_v1.01.fasta.fai

  • Assembly from 20200923

    • Q7-filtered NanoPore data. Includes Hematodinium-infected sample.

    • Subset of cbai_genome_v1.0.fasta with contigs >1000bp

• cbai_genome_v1.0.fasta (19MB)

  • MD5 = 2f3b651bb0b875b0287e71e315cad59a

  • BUSCOs: C:0.4%[S:0.3%,D:0.1%],F:0.3%,M:99.3%,n:978

  • FastA index (samtools faidx)

    • cbai_genome_v1.0.fasta.fai

  • Assembly from 20200917

    • Q7-filtered NanoPore data. Includes Hematodinium-infected sample.

Transcriptomes

• RNA-seq sample list

• cbai_transcriptome_v3.1.fasta

  • MD5 = aeec8ffbf8fa44fb1750caee6abaf68a

  • BUSCOs: C:96.5%[S:40.3%,D:56.2%],F:2.2%,M:1.3%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v3.1.fasta.fai

  • BLASTx annotation (outfmt6)

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-UW with non_Alveolata. Derived from cbai_transcriptome_v3.0.fasta

• cbai_transcriptome_v3.0.fasta

  • Assembly from 20200518

  • MD5 = 5516789cbad5fa9009c3566003557875

  • BUSCOs: C:97.6%[S:39.1%,D:58.5%],F:1.6%,M:0.8%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v3.0.fasta.fai

  • BLASTx annotation (outfmt6)

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-UW with no taxonomic filter.

• cbai_transcriptome_v2.1.fasta

  • MD5 = 1fb788175f9bb7cd5145370a399ae857

  • BUSCOs: C:98.3%[S:25.2%,D:73.1%],F:1.4%,M:0.3%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v2.1.fasta.fai

  • BLASTx annotation

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-GW, 2020-UW with non_Alveolata. Derived from cbai_transcriptome_v2.0.fasta

• cbai_transcriptome_v2.0.fasta

  • Also referred to as 20200507.C_bairdi.Trinity.fasta.

  • MD5 = 01adbd54298495c147767b19ee5c0de9 https://gannet.fish.washington.edu/Atumefaciens/20200526_cbai_trinotate_transcriptome-v3.0/20200526.cbai.trinotate.go_annotations.txt

  • BUSCOs: C:98.8%[S:24.9%,D:73.9%],F:0.9%,M:0.3%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v2.0.fasta.fai

  • BLASTx annotation

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-GW, 2020-UW with no taxonomic filter.

• cbai_transcriptome_v1.7.fasta

  • MD5 = 032d1f81c7744736ebeefe7f63ed6d95

  • Assembly from 20200527

  • FastA index (samtools faidx)

    • cbai_transcriptome_v1.7.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v1.7.fasta.fai

  • BUSCOs: C:86.7%[S:66.5%,D:20.2%],F:8.2%,M:5.1%,n:978

  • BLASTx Annotation (outfmt6)

  • [GO Terms Annotation] (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-UW with Arthropoda only reads.

• cbai_transcriptome_v1.6.fasta

  • MD5 = 46d77ce86cdbbcac26bf1a6cb820651e

  • FastA index (samtools faidx)

    • cbai_transcriptome_v1.6.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v1.6.fasta.fai

  • BUSCOs: C:91.7%[S:62.6%,D:29.1%],F:6.2%,M:2.1%,n:978

  • BLASTx Annotation (outfmt6)

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-GW, 2020-UW with Arthropoda only reads.

• cbai_transcriptome_v1.5.fasta

  • MD5 = e61d68c45728ffbb91e3d34c087d9aa9

  • BUSCOs: C:91.8%[S:64.0%,D:27.8%],F:5.9%,M:2.3%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v1.5.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v1.5.fasta.fai

  • Updated assembly from 20200330. Also referred to as 20200408.C_bairdi.megan.Trinity.fasta

  • BLASTx Annotation

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019, 2020-GW with Arthropoda only reads.

• cbai_transcriptome_v1.0.fasta

  • MD5 = fb28a203154b44b67ec2e2476d96d326

  • BUSCOs: C:85.5%[S:64.7%,D:20.8%],F:9.3%,M:5.2%,n:978

  • FastA index (samtools faidx)

    • cbai_transcriptome_v1.0.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v1.0.fasta.fasta.fai

  • Initial Trinity assembly from 20200122

  • BLASTx Annotation

  • GO Terms Annotation (Trinotate)

  • internal short-hand: includes 2018, 2019 with Arthropoda only reads.

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Crassostrea gigas

Related Resources

• Compilation of DNA Methylation Genome Feature Tracks (Crassostrea gigas) circa 2015

• Re-defining Cgigas Canonical features circa 2015

• Gigaton

• TJGR

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:

• Crassostrea_gigas.oyster_v9.dna_sm.toplevel_bisulfite.tar.gz : http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel_bisulfite.tar.gz

  • Gzipped tarball of bisulfite genome for use with Bismark
  • Creation details here

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

  • Contains Tandem Repeats and wublastx features.

• 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

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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)

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

• 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

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Hematodinium sp. (Host: Chionoecetes bairdi)

Transcriptomes

• hemat_transcriptome_v1.5.fasta

  • MD5 = b8d4a3c1bad2e07da8431bf70bdabfdd

  • BUSCOs: C:25.6%[S:20.7%,D:4.9%],F:11.7%,M:62.7%,n:978

  • FastA index (samtools faidx)

    • hemat_transcriptome_v1.5.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/hemat_transcriptome_v1.5.fasta.fai

  • Updated assembly from 20200330.

  • BLASTx Annotation (txt; 355KB)

  • Trinotate GO Terms Annotation (txt; 2.3MB)

  • internal short-hand: includes 2018, 2019, 2020-GW with Alveolata only reads.

• hemat_transcriptome_v1.0.fasta (3.9MB)

  • MD5 = fa5eb74767d180af5265d2d1f80b6430

  • BUSCOs: C:25.1%[S:19.2%,D:5.9%],F:9.5%,M:65.4%,n:978

  • FastA index (samtools faidx)

    • hemat_transcriptome_v1.0.fasta.fai : https://owl.fish.washington.edu/halfshell/genomic-databank/hemat_transcriptome_v1.0.fasta.fai

  • Initial Trinity assembly from 20200122

  • BLASTx Annotation (txt; 308KB)

  • Trinotate GO Terms Annotation (txt; 2.1MB)

  • internal short-hand: includes 2018, 2019 with Alveolata only reads.

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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

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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:

• Olurida_transcriptome_v3.fasta

  • MD5 = 9da3242af2be0463051ec7e1f39b2593

Tissue-specific transcriptomes generated by Katherine Silliman

• Olurida_CA_adductor_Trinity.fasta.gz

• Olurida_CA_ctenidia_Trinity.fasta.gz

• Olurida_CA_mantle_Trinity.fasta.gz

• Olurida_gonad_Trinity.fasta.gz

Genome Feature Tracks

• Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff (2.9GB) : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff

  • MD5 = f54512bd964f45645c34b1e8e403a2b0

• Olurida_v081-20190709.CDS.gff : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081-20190709.CDS.gff

• Olurida_v081-20190709.exon.gff : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081-20190709.exon.gff

• Olurida_v081-20190709.gene.gff : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081-20190709.gene.gff

• Olurida_v081-20190709.mRNA.gff : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081-20190709.mRNA.gff

• Olurida_v081_TE-Cg.gff : http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081_TE-Cg.gff

  • MD5 = 977fd7cdb460cd0b9df5e875e1e880ea

  • Transposable Element track - more details in Sam's Notebook, including a summary table.

• Olurida_v081_CG-motif.gff : https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081_CG-motif.gff

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Panopea generosa

Genome:

• Pgenerosa_v074.fa : http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v074.fa

  • ENA Accession: GCA_902825435

  • Version of 070 containing 18 largest scaffolds (details on subsetting)

  • MD5 = 32976550b9030126c07920d5f2db179c

  • BUSCO scores:

    • C:71.6%[S:70.7%,D:0.9%],F:4.7%,M:23.7%,n:978
    • Notebook entry

  • FastA index (samtools faidx) - http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v074.fa.fai

Bisulfite Genome

Genome Feature Tracks

Panopea-generosa-vv0.74.a3

• These originate from GenSAS annotation on 20190710

• BUSCO:

  • 68.4% complete BUSCOs

• Panopea-generosa-vv0.74.a3.gene.gff3 : https://owl.fish.washington.edu/halfshell/genomic-databank/Panopea-generosa-vv0.74.a3.gene.gff3

  • code

• Panopea-generosa-vv0.74.a3.exon.gff3 : https://owl.fish.washington.edu/halfshell/genomic-databank/Panopea-generosa-vv0.74.a3.exon.gff3

  • code

• Panopea-generosa-vv0.74.a3.intragenic.bed : https://gannet.fish.washington.edu/seashell/wd/091319/tracks/Panopea-generosa-vv0.74.a3.intragenic.bed

• Panopea-generosa-vv0.74.a3.intron.bed : https://gannet.fish.washington.edu/seashell/wd/091319/tracks/Panopea-generosa-vv0.74.a3.intron.bed

• Panopea-generosa-vv0.74.a3.rm.gff3 : https://gannet.fish.washington.edu/seashell/wd/091319/tracks/Panopea-generosa-vv0.74.a3.rm.gff3

  • index: https://gannet.fish.washington.edu/seashell/wd/091319/tracks/Panopea-generosa-vv0.74.a3.rm.gff3.idx

• Pgenerosa_v074.CpG.gff : https://gannet.fish.washington.edu/seashell/wd/091319/tracks/Pgenerosa_v074.CpG.gff

• Panopea-generosa-vv0.74.a3.CDS.gff3 : https://owl.fish.washington.edu/halfshell/genomic-databank/Panopea-generosa-vv0.74.a3.CDS.gff3

  • code

• Panopea-generosa-vv0.74.a3.mRNA.gff3 : https://owl.fish.washington.edu/halfshell/genomic-databank/Panopea-generosa-vv0.74.a3.mRNA.gff3

  • code

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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

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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.

• QPX_v017.fasta : https://ndownloader.figshare.com/files/3085550

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.

• QPX_v015.fasta : https://doi.org/10.1371/journal.pone.0074196.s001

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_v1_clean.fasta

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.

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