eggnog‐diamond‐search - bokulich-lab/q2-annotate GitHub Wiki

Find homolog sequences in contigs or MAGs against a Diamond reference database.

For the full description of the action's inputs, outputs and parameters run qiime moshpit eggnog‐diamond‐search --help in the terminal.

Inputs

• sequences (SampleData[Contigs] | FeatureData[MAG]): MAGs or contigs to search for homolog sequences against a Diamond database.
• diamond-db (ReferenceDB[Diamond]): Diamond reference database.

Outputs

• eggnog-hits (SampleData[BLAST6]): Predicted hits. For each FASTA file in the input, a table is generated where every row is a hit (a predicted homolog) and columns are information about that specific hit/alignment. These tables or table, depending on whether there are multiple fasta files in the input, are all contained in this output artifact. For more information about these tables take a look at the Diamond documentation.
• table (FeatureTable[Frequency]): Feature table with counts of orthologs per sample/MAG.

Example Use

qiime moshpit eggnog-diamond-search \
   --i-sequences mags.qza \
   --i-diamond-db diamond_db.qza \
   --o-eggnog-hits hits.qza \
   --o-table table.qza \
   --verbose

Tutorials

List of tutorials that involve this action.

• Functional Annotation of MAGs (or Contigs)

Links to Relevant Resources

• eggnog-mapper
• Diamond

Citation

@article{key0,
 author = {Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg},
 copyright = {2021 The Author(s)},
 doi = {10.1038/s41592-021-01101-x},
 issn = {1548-7105},
 journal = {Nature Methods},
 keywords = {Computational biology and bioinformatics, Genome informatics, Genomic analysis, Sequencing, Software},
 language = {en},
 month = {April},
 note = {Number: 4},
 number = {4},
 pages = {366--368},
 publisher = {Nature Publishing Group},
 title = {Sensitive protein alignments at tree-of-life scale using DIAMOND},
 url = {https://www.nature.com/articles/s41592-021-01101-x},
 urldate = {2023-12-01},
 volume = {18},
 year = {2021}
}

@article{key1,
 author = {Huerta-Cepas, Jaime and Szklarczyk, Damian and Heller, Davide and Hernández-Plaza, Ana and Forslund, Sofia K and Cook, Helen and Mende, Daniel R and Letunic, Ivica and Rattei, Thomas and Jensen, Lars J and von Mering, Christian and Bork, Peer},
 doi = {10.1093/nar/gky1085},
 issn = {0305-1048},
 journal = {Nucleic Acids Research},
 month = {January},
 number = {D1},
 pages = {D309--D314},
 shorttitle = {eggNOG 5.0},
 title = {eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses},
 url = {https://doi.org/10.1093/nar/gky1085},
 urldate = {2024-01-18},
 volume = {47},
 year = {2019}
}