C-CoMP AE2504 BATS/Hydrostation S Area 15m Long-Read Metagenome Assembly Anvi'o Contigs Database

This record contains an anvi'o contigs database generated from a long-read metagenome collected during NSF Center for Chemical Currencies of a Microbial Planet (C-CoMP) RV Atlantic Explorer cruise AE2504 by the Autonomous Underwater Vehicle (AUV) Clio at 15m depth from 32°6.18042’N 063°37.44348’W (the area of the Bermuda Atlantic Time Series and Hydrostation S) on March 15, 2025 at 02:05:36 UTC. A 0.2-51µm fraction was taken from 116.1L of filtered seawater. Part of the filter was used in long-read sequencing using three PacBio SMRT flow cells done by Bruno Huettel and colleagues at the Max Planck Genome Center Cologne. Reads were assembled from the three replicate sequencing batches using hifiasm-meta: 29,769,307 reads containing 181,273,171,831 bp, for a mean read length of 6 kbp, were assembled into 359,745 contigs containing 12,141,101,203 bp, for a mean contig length of 34 kbp. Here are the DOIs of Zenodo records for associated long-read metagenomic databases:BATS_15032025_15m (currently viewing): 10.5281/zenodo.20724152LTER_20032025_15m: 10.5281/zenodo.20724154BATS_06092025_15m: 10.5281/zenodo.20724156LTER_14092025_15m: 10.5281/zenodo.20724162EDDY_10092025_67m: 10.5281/zenodo.20724166BATS_05092025_200m: 10.5281/zenodo.20724069 TSV files originating from `anvi-display-contig-stats` contain summary statistics for this and associated metagenomes of assembled contigs (`contig_summary.tsv`), gene calls in contigs (`gene_summary.tsv`), and estimated numbers of genomes from single copy core genes (`genome_summary.tsv`). Shell scripts allow replication of the computational workflow, including metagenome assembly and generation of the databases: 1) `submit_hifiasm_meta.sh` for assembly, 2) `finalize_assemblies.sh` for assembly output formatting, and 3) `generate_contigs_dbs.sh` for contigs generation from the assembly FASTA. Here is an example of an anvi'o command interfacing with the database, showing how to extract gene calls as amino acid sequences:anvi-get-sequences-for-gene-calls -c BATS_15032025_15m.db --get-aa-sequences -o BATS_15032025_15m.faa We encourage use of this database with proper attribution to the Center for Chemical Currencies of a Microbial Planet (C-CoMP) per licensing requirements. If you are using this database, please include a citation for this Zenodo record in your work. We also encourage that you contact C-CoMP with questions and to notify us that you are using the database by emailing C-CoMP Digital Coordinator Laura Gray at [e-mail].