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18s_sequencing_bias_determination_ga03_gp13

A forever home for notes associated with calculating the 18S biases for GA03/GP13 cruises from the BioGEOTRACES campaign.

515f-y_926r_database_construction

A repository containing code for constructing qiime2 databases for the "Parada primers" (515F-Y / 926R). See linked OSF repo for the actual artifacts for specific qiime2 versions.

academic-kickstart

Easily create a beautiful website using Academic and Hugo

academic-kickstart-fuhrmanlab

asvtosag

A rough workflow for extracting SSU rRNA from SAGs, blasting ASVs against them, running growthpred (Vieira-Silva and Rocha 2010, https://doi.org/10.1371/journal.pgen.1000808), and then generating a summary output. Currently set up to work for GORG SAGs (Pachiadaki et al 2019; doi: 10.1016/j.cell.2019.11.017)

bbbtutorial

cmap-geotraces-sw-data-parsing

Scripts for parsing IDP 2021 / BODC websites with the goal of obtaining instrument information for CMAP's ingestion of these datasets. Also contains some limited number of output files from the analysis as well as conda YAML files for reproducibility/documentation.

ctdprs2depth

How to convert CTD pressure to depth with pyseawater, taking CTDPRS and latitude as arguments.

darwin-asv-plots

Some scripts for making comparisons between DARWIN model output and ASV data and generating visualizations with seaborn. Uses jupyter notebooks.

demux-notes

Notes on demultiplexing 515Y reads with cutadapt

demux-udi-from-undetermined

A hacky workflow for demultiplexing dual-indexed reads as might be spat out by bcl2fastq when run with an empty sample sheet.

easv-pipeline-for-515y-926r

This is a collection of scripts for analyzing mixed 16S/18S amplicon sequences using tools such as qiime2, DADA2, deblur, and bbtools

eukulele_review

ga02watercolumncharacterization

Scripts and documentation for getting metadata associated with the GEOTRACES GA02 cruise, with the goal of associating these environmental data with microbial distributional data.

ga03_gp13_515y-926r_cmap

Code for processing amplicons associated with BioGEOTRACES cruises GA03 and GP13 prior to ingestion into CMAP

ga10watercolumncharacterization

Notes for lining up CTD profiles with molecular data so we can characterize the part of the water column microbial community data is derived from.

git-storage

github-utilities

global-rrna-univeral-metabarcoding-of-plankton

A central repository for the GRUMP (Global rRNA Universal Metabarcoding of Plankton) dataset, containing scripts for bioinformatic processing and retrieval of associated physical / geochemical measurements from publicly available data.

gtdb-ssu-filtering

A basic script for filtering phylogenetic incongruencies from GTDB SSU rRNA sequences according to SILVA classifications of the same using RDP classifier vs SILVA v132

hugo-academic

📝 The website builder for Hugo. Build and deploy a beautiful website in minutes!

i9n-i8s_water_column_characterization

Notes for lining up CTD profiles with molecular data so we can characterize the part of the water column microbial community data is derived from.

in-silico-mocks

Backup for in-silico mocks (2021-02-23)

jcmcnch.github.io

Website

ks_anvio_analysis

Scripts to reproduce anvi'o pangenome analysis for Kueishan pangenomes from campylobacterial chemoautotrophic isolates

mag_postbin_processing

merge-svgs

notes on how to merge svgs horizontally

mgprimereval

This is a snakemake pipeline that determines primer mismatches to SSU rRNA in metagenomic data.

microheterotrophmodelling

A repository to store code linking unfractionated (>0.2µm) amplicon sequencing data from GO-SHIP (P16N/S, I8/I9) and BioGEOTRACES GA02 basin-scale transects to genome sequences from GTDB, and separating them into broader, order-level categories to view biogeographic distributions in comparison to model results.

mosaic_water_column_characterization

A home for making plots to characterize discrete MOSAiC samples in the context of water column properties.