Taxonomy

Metdbid	METDB_00002
Kingdom	Eukaryota
Supergroup	Alveolata
Phylum	Dinoflagellata
Class	Dinophyceae
Order	Dinophyceae_X
Family	Dinophyceae_Xx
Genus	Akashiwo
Species	sanguinea
Strain name	CCCM885
Strain name synonyms	syn. UW496
TaxNCBI	143672
TaxWoRMS	232546
Readset (paired)	MMETSP0223_2 - SRR1294461
Readset (paired)	MMETSP0223_2 - SRR1294462
Readset (paired)	MMETSP0223_2 - SRR1294463
Readset (paired)	MMETSP0223_2 - SRR1294464
Annotation search	Link to associated annotation search function

Environmental parameters

Longitude	-3.97
Latitude	48.73
Site	North Atlantic
Site description	Roscoff; France
Country	FRANCE
Habitat	marine habitat

Assembly metrics

Percentage of remapping of all readsets on transcriptom	13.5%
Number of contigs	3
Largest contig	100,286
Number of bases	132,250
Contigs average lenght	43900.3
Number of contigs with orf	3
n50	100,286
GC	0.47657
Transcriptome analysis project	Cohen Lisa, C.Titus et al
Origin of the datasets	MMETSP
Assembly Type	paired
Trinity version	trinity-v2.2.0

Annotation metrics

Transdecoder: Number of predicted proteins	316
BUSCO against eukaryota_odb9	Complete BUSCOs 0.00% (0) Complete and single-copy BUSCOs 0.00% (0) Complete and duplicated BUSCOs 0.00% (0) Fragmented BUSCOs 0.33% (1) Missing BUSCOs 99.67% (302) Total BUSCO groups searched 100.00% (303)
Interproscan: Number of proteins with interproscan match	Pfam 67 Interproscan ID 182 Gene ontology ID 144.0 KEGG ID 4.0 PRINTS 50
Cmsearch	tRNA 0 tmRNA 0 SSU_rRNA_eukarya 9 LSU_rRNA_eukarya 22 5_8S_rRNA 0 Others 66
Diamond against Uniref90_v7-2019	1493

Associated result files

Reference Assembly

Contigs fasta file	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired.fasta

Reads remapping to assembly

Metadata info (json)	MMETSP_akashiwo-sanguinea-syn.-uw496_mmetsp0223_salmon-v0.9.1_lisac.json
Quantification file (sf)	quant.sf

Assembly metrics

Contigs metrics (csv)	contigs.csv
Assembly metrics file (csv)	assemblies.csv

Annotation files

Diamond: for aligning Transcripts against NCBI NR	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired.diamond_matches
BUSCO: assessment of transcriptome completeness	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired_BUSCO_short_summary.txt
Cmsearch: Use of Covariance model (CM) to search for homologous RNAs Within Transcriptoms	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired_cat_cmsearch_matches.tbl.deoverlapped
Transdecoder: Find Coding Regions Within Transcripts	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired_cut.cleaned.fasta.transdecoder.pep
InterProscan: Protein sequence analysis and classification	MMETSP-METDB_00002-akashiwo-sanguinea-syn.uw496-paired_full_i5_annotations

Quality file

Read quality file	SRR1294464_1_fastqc.zip
Read quality file	SRR1294461_1_fastqc.zip
Read quality file	SRR1294462_1_fastqc.zip
Read quality file	SRR1294463_1_fastqc.zip

Additional result files (complete list)

MMETSP decontaminated contigs using MMETSP Cleanup algorithm [3]	MMETSP0223_clean.fasta
Re-assembled contigs by Lisa K. Johnson [1] using the readsets generated by the MMETSP project [2]	MMETSP_akashiwo-sanguinea-syn.-uw496-15-8-125-ply-372-ccap66-9_mmetsp0223_trinity-v2.2.0_lisac.fasta.tar.gz