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Draft Protocol for Assembling MAGs from Complex Metagenomes
My latest workflow for QAQC, assembly, binning, taxnomic annotation, and functional annotation of environmental metagenomes. It is still in draft form and I’m getting all the pipeline/nextflow scripts together.
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Processing R1, R2, and Index Files to be used with DADA2
Demultiplexing Illumina Sequences from the old 3-file systems. Here specifically to import into dada2 and upload to NCBI.
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Installing rstudio and dada2 on our new server
Troubleshooting to install dada2 and rstudio on our local server using conda.
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Using Conda Sop
Using Conda to Manage your Environments and ProgramsEverything you could ever want to know can be found in the anaconda documents. This will just serve as a very quick guide on installing programs using conda and keeping your account /computer nice and organized without conflicts.
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Playing with R and (ana/mini)conda
Short post for helping an R environment play well with a different R install.
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Snakemake pipeline for 16S rRNA amplicon analysis
Trying to simplify my hacked together analysis pipeline with something a little more robust. Plus I’ve been wanting to play with snakemake for a long time now.
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RaXML-EPA and iTOL
Inserting and visualizing short read sequences into a curated phylogenetic tree using RaXML-EPA and the interactive tree of life.
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Testing Megahit metagenomic assembly & binning approachs on subsampled metagenomes
I’m using what I learned from the metagenomic assembly testing to do a more involved run on a subset of the data while I wait for resources on the cluster to become available to run the full dataset.
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Large-scale OTU picking with SWARM (SUCCESS!)
Successfully picking OTUs using the SWARM algorithm on a large diverse set of 16S amplicons.
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Many failed attempts to cluster large 16S sequence dataset
This is about a months worth of failed attempts to pick operational taxonomic units on a 78 million sequence database of 16S sequences. I explore the use of greedy and hierarchal clustering approaches from MOTHUR to QIIME pathways.
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Refining 16S Analysis for Deep Ocean Sediments
Tracking progress on finalizing deep ocean 16S sequence analysis
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Managing this website with Git and Github
Hosting this website on Github and working with git version control.
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Testing Metagenomic Assemblers
Testing out and learning to use some Metagenomic assemblers. Starting with IDBA-UD, SPAdes, and Velvet. Will be progressing to binning and de novo genome construction next.