[Microbial Diversity Course](http://www.mbl.edu/microbialdiversity/), [Marine Biological Lab](http://www.mbl.edu) Microbial community samples collected from the Trunk River in Woods Hole, MA 2014-. This data archive includes: - ssu rRNA amplicon raw data and analyses - metagenomic assemblies and genomes - analytical data from sites - bacteria/archaeal/eukaryotic isolates and individual genomes - links to MicDiv Course reports from this site - links to publications this site > NOTE: raw genomic/transcriptomic data are uploaded to the SRA Archives ---------- **Selected Course pubs about Trunk River microbes** Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom Srijak Bhatnagar, Elise S. Cowley, Sebastian H. Kopf, Sherlynette Pérez Castro, Sean Kearney, Scott C. Dawson, Kurt Hanselmann & S. Emil Ruff (2020) [Environmental Microbiome volume 15, 3][1] ---------- Click here for 2015 [Amplicon analysis files, Krona plots](https://github.com/mblmicdiv/TrunkRiver_amplicon_analysis) generated from QIIME. Click here for other (2018-) Amplicon analysis files, Krona plots 16S metadata files: * [MiSeq_metadata.xlsx](https://osf.io/4srqn/), supplemental single MiSeq reads from 2014 and 2015 * [MOist LEMon Data Log.xlsx](https://osf.io/2bjym/), paired MiSeq reads from 2015 Click here for 2015 [MG-RAST analyses for assemblies by individual file](http://metagenomics.anl.gov/mgmain.html?mgpage=project&project=mgp81845). ---- 2015 Assemblies done using: ``` ~/research/megahit/megahit -1 7A3_R1.fastq.gz,7E3_R1.fastq.gz,7K3_R1.fastq.gz,SK_R1.fastq.gz -2 7A3_R2.fastq.gz,7E3_R2.fastq.gz,7K3_R2.fastq.gz,SK_R2.fastq.gz -o trunk_assembly extract-long-sequences.py trunk_assembly/final.contigs.fa -l 500 > trunk_assembly.500.fa gzip trunk_assembly500.fa.gz ``` ---- 2021 Work done by Trina * QC done with fastp * Assembly done with SPAdes-3.13.1 (meta) * Binning done with Metabat-2.12.1 Details are in included README files [1]: https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-019-0348-0