Assembly Summary


Taxonomy

Metdbid METDB_00008
Kingdom Eukaryota
Supergroup Alveolata
Phylum Dinoflagellata
Class Dinophyceae
Order Dinophyceae_X
Family Dinophyceae_Xx
Genus Alexandrium
Species monilatum
Strain name CCMP3105
Strain name synonyms syn. AM01
TaxNCBI 311494
TaxWoRMS 231875
Readset (paired) MMETSP0093 - SRR1296895
Readset (paired) MMETSP0095 - SRR1296896
Readset (paired) MMETSP0096 - SRR1296897
Readset (paired) MMETSP0097 - SRR1296898
Annotation search Link to associated annotation search function

Environmental parameters

Longitude -89.0761
Latitude 30.0417
Site North Atlantic
Site description Off Gulfport; Mississippi; USA
Country UNITED STATES
Habitat marine habitat

Legend for assembly and annotation metrics
  • Good
  • Acceptable
  • Bad

Assembly metrics

Percentage of remapping of all readsets on transcriptom 89.7%
Percentage of good mapping 79
Number of contigs 128,815
Largest contig 11,495
Number of bases 130,346,526
Contigs average lenght 1011.9
Number of contigs with orf 81,467
n50 1,523
GC 0.6654100000000001
Transcriptome analysis project Arnaud Meng Thesis
Origin of the datasets MMETSP
Assembly Type paired
Trinity version trinity-v2.6.5

Krona

Annotation metrics

Transdecoder: Number of predicted proteins 90326
BUSCO against eukaryota_odb9
Complete BUSCOs 80.53% (244)
Complete and single-copy BUSCOs 54.13% (164)
Complete and duplicated BUSCOs 26.40% (80)
Fragmented BUSCOs 3.63% (11)
Missing BUSCOs 15.84% (48)
Total BUSCO groups searched 100.00% (303)
Interproscan: Number of proteins with interproscan match
Pfam 63762
Interproscan ID 172368
Gene ontology ID 94853.0
KEGG ID 6682.0
PRINTS 24905
Cmsearch
tRNA 11
tmRNA 8
SSU_rRNA_eukarya 8
LSU_rRNA_eukarya 25
5_8S_rRNA 1
Others 210
Diamond against Uniref90_v7-2019 243794


Associated result files


Reference Assembly

Contigs fasta file MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired.fasta

Reads remapping to assembly

Quantification file (sf) quant.sf
Metadata info (json) MMETSP_alexandrium-monilatum-ccmp3105_salmon-v0.9.1_elixir.json

Assembly metrics

Contigs with bad mapping (fasta) bad.METDB-00008_alexandrium-monilatum-syn.am01.fasta.gz
Contigs metrics (csv) contigs.csv
Contigs with good mapping (fasta) good.METDB-00008_alexandrium-monilatum-syn.am01.fasta.gz
Assembly metrics file (csv) MMETSP_alexandrium-monilatum-ccmp3105_transrate-v1.0.2_elixir.csv

Annotation files

Cmsearch: Use of Covariance model (CM) to search for homologous RNAs Within Transcriptoms MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired_cat_cmsearch_matches.tbl.deoverlapped
BUSCO: assessment of transcriptome completeness MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired_BUSCO_short_summary.txt
InterProscan: Protein sequence analysis and classification MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired_full_i5_annotations
Transdecoder: Find Coding Regions Within Transcripts MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired_cut.cleaned.fasta.transdecoder.pep
Diamond: for aligning Transcripts against NCBI NR MMETSP-METDB_00008-alexandrium-monilatum-syn.am01-paired.diamond_matches

Quality file

Read quality file SRR1296897_1_fastqc.zip
Read quality file SRR1296895_1_fastqc.zip
Read quality file SRR1296896_1_fastqc.zip
Read quality file SRR1296898_1_fastqc.zip

Reads dissimilarity evaluation

Presence-absence-based Bray-Curtis distance matrix mat_presenceAbsence_braycurtis.csv.gz
Abundance-based Bray-Curtis distance matrix mat_abundance_braycurtis.csv.gz

Ribosomal ribonucleic acid retrieved from assembly

rRNA result file (gff) MMETSP_alexandrium-monilatum-ccmp3105_rnammer-v1.2_elixir.gff

Additional result files (complete list)

Re-assembled contigs by Lisa K. Johnson [1] using the readsets generated by the MMETSP project [2] MMETSP_alexandrium-monilatum-ccmp3105_mmetsp0097_trinity-v2.2.0_lisac.fasta.tar.gz
MMETSP decontaminated contigs using MMETSP Cleanup algorithm [3] MMETSP0093_clean.fasta
MMETSP decontaminated contigs using MMETSP Cleanup algorithm [3] MMETSP0095_clean.fasta
MMETSP decontaminated contigs using MMETSP Cleanup algorithm [3] MMETSP0096_clean.fasta
Re-assembled contigs by Lisa K. Johnson [1] using the readsets generated by the MMETSP project [2] MMETSP_alexandrium-monilatum-ccmp3105_mmetsp0095_trinity-v2.2.0_lisac.fasta.tar.gz
MMETSP decontaminated contigs using MMETSP Cleanup algorithm [3] MMETSP0097_clean.fasta
Re-assembled contigs by Lisa K. Johnson [1] using the readsets generated by the MMETSP project [2] MMETSP_alexandrium-monilatum-ccmp3105_mmetsp0096_trinity-v2.2.0_lisac.fasta.tar.gz
Re-assembled contigs by Lisa K. Johnson [1] using the readsets generated by the MMETSP project [2] MMETSP_alexandrium-monilatum-ccmp3105_mmetsp0093_trinity-v2.2.0_lisac.fasta.tar.gz